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Folder iconTutorial Collection

Rahul Arora
April 22, 2020
This is a model tutorial collection to demonstrate how to analyse iCLIP data using the iMaps platform.

demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch.fastq.gz
29.70 MB
demux_nomatch_fastqc.zip
461.37 kB

PTBP1_Hela_WT_20110427_LUjh27

FASTQ file (CLIP)
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27.fastq.gz
347 B
ptbp1-hela-wt-20110427-lujh27_fastqc.zip
696.21 kB
Paraclu
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
89 B
Cutadapt (single-end)
report.txt
668 B
ptbp1-hela-wt-20110427-lujh27_trimmed.fastq.gz
329 B
fastqc
Directory
STAR
ptbp1-hela-wt-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
83 B
ptbp1-hela-wt-20110427-lujh27_trimmed.bam.bai
126.52 kB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam
3.71 kB
ptbp1-hela-wt-20110427-lujh27_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27_trimmed_SJ.out.tab
74 B
ptbp1-hela-wt-20110427-lujh27_trimmed.bw
15.51 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bed.gz
120 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
250 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
126 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bedgraph
260 B
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.tar.gz
957 B
iCount summary
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
196 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
79 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
292 B

Group_Analysis_PTBP1_Merged_Replicates

iCount summary
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_gene.tsv
1.91 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_type.tsv
440 B
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_subtype.tsv
1.01 kB
Paraclu
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_peaks.bed.gz
738.13 kB
PEKA
4mer analysis of Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.tar.gz
759.51 kB
iCount annotate
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_annotated.bedgraph
158.23 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_annotated.bed.gz
39.63 MB
iCount group
Group_Analysis_PTBP1_Merged_Replicates_grouped_reads.bed.gz
32.90 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.bedgraph
158.23 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.bed.gz
32.68 MB
iCount RNA-maps
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.tar.gz
1.63 MB

PTBP1_iCLIP1_data.fastq.gz

FASTQ file (single-end)
fastqc
Directory
PTBP1_iCLIP1_data_fastqc.zip
509.12 kB
PTBP1_iCLIP1_data.fastq.gz
487.35 MB
stderr.txt
1015 B

PTBP1_Hela_WT_noAB_20110427_LUjh27

FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-noab-20110427-lujh27.fastq.gz
1.05 MB
stderr.txt
1.32 kB
ptbp1-hela-wt-noab-20110427-lujh27_fastqc.zip
354.02 kB
iCount summary
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
414 B
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
900 B
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
437.34 kB
iCount RNA-maps
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.tar.gz
414.55 kB
Paraclu
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
284 B
PEKA
4mer analysis of ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome.tar.gz
164 B
Cutadapt (single-end)
report.txt
669 B
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.fastq.gz
1.01 MB
fastqc
Directory
STAR
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bam.bai
1.78 MB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
152.64 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bam
2.52 MB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_SJ.out.tab
4.90 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_stats.txt
1.79 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bw
22.52 kB
iCount xlsites
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.bed.gz
113.92 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_skipped.bam
2.90 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.bedgraph
434.49 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
215.26 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
115.58 kB
iCount peaks
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_scores.tsv.gz
155.82 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bedgraph
8.12 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
3.24 kB

PTBP1_Hela_WT_20110427_LUjh27

FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27.fastq.gz
85.32 MB
stderr.txt
1.23 kB
ptbp1-hela-wt-20110427-lujh27_fastqc.zip
335.06 kB
iCount summary
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
1016 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
431 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
1.42 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
102.78 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.tar.gz
895.61 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
664 B
ptbp1-hela-wt-20110427-lujh27_trimmed.fastq.gz
86.47 MB
STAR
ptbp1-hela-wt-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
11.36 MB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam
146.28 MB
ptbp1-hela-wt-20110427-lujh27_trimmed_SJ.out.tab
185.52 kB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam.bai
3.80 MB
ptbp1-hela-wt-20110427-lujh27_trimmed_stats.txt
1.80 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_skipped.bam
3.49 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bed.gz
8.58 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
8.64 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
12.71 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bedgraph
40.72 MB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27_mapped_to_genome.tar.gz
439.68 kB
iCount peaks
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bedgraph
2.74 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
677.60 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_scores.tsv.gz
6.63 MB

PTBP1_Hela_WT_20110427_LUjh27_2

FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.26 kB
ptbp1-hela-wt-20110427-lujh27-2_fastqc.zip
335.50 kB
ptbp1-hela-wt-20110427-lujh27-2.fastq.gz
51.86 MB
Cutadapt (single-end)
report.txt
666 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-2_trimmed.fastq.gz
52.09 MB
STAR
ptbp1-hela-wt-20110427-lujh27-2_trimmed_unmapped.out.mate1.fastq.gz
7.38 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bam.bai
3.69 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bam
88.86 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed_stats.txt
1.80 kB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bw
69.63 kB
ptbp1-hela-wt-20110427-lujh27-2_trimmed_SJ.out.tab
107.79 kB
iCount summary
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_type.tsv
429 B
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_gene.tsv
1.27 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_subtype.tsv
1009 B
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_skipped.bam
3.24 kB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.bed.gz
5.03 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.bedgraph
23.54 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_singleAndMulti.bed.gz
7.62 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_reads_single.bed.gz
5.08 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bed.gz
42.18 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.tar.gz
733.17 kB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome.tar.gz
394.24 kB
iCount peaks
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bed.gz
281.20 kB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_scores.tsv.gz
4.00 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bedgraph
1.04 MB

PTBP1_Hela_WT_20110427_LUjh27_3

FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.26 kB
ptbp1-hela-wt-20110427-lujh27-3.fastq.gz
81.06 MB
ptbp1-hela-wt-20110427-lujh27-3_fastqc.zip
335.37 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
666 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.fastq.gz
82.24 MB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_skipped.bam
3.32 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_singleAndMulti.bed.gz
12.34 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bed.gz
8.24 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_reads_single.bed.gz
8.30 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bedgraph
38.99 MB
STAR
ptbp1-hela-wt-20110427-lujh27-3_trimmed_unmapped.out.mate1.fastq.gz
11.61 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam
142.46 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam.bai
3.76 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_stats.txt
1.80 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_SJ.out.tab
193.95 kB
iCount summary
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_gene.tsv
1.43 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_type.tsv
434 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_subtype.tsv
1012 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
91.16 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.tar.gz
914.72 kB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome.tar.gz
416.27 kB
iCount peaks
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bedgraph
2.40 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
602.09 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_scores.tsv.gz
6.39 MB

PTBP1_Hela_WT_noAB_20110427_LUjh27

FASTQ file (CLIP)
ptbp1-hela-wt-noab-20110427-lujh27.fastq.gz
37 B

PTBP1_Hela_WT_20110427_LUjh27_2

FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-2.fastq.gz
37 B

PTBP1_Hela_WT_20110427_LUjh27_3

FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-3.fastq.gz
268 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-3_fastqc.zip
702.63 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.tar.gz
959 B
Cutadapt (single-end)
report.txt
671 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.fastq.gz
250 B
fastqc
Directory
STAR
ptbp1-hela-wt-20110427-lujh27-3_trimmed_unmapped.out.mate1.fastq.gz
204 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam.bai
6.08 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam
3.59 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_SJ.out.tab
0 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bw
15.54 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bed.gz
80 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_singleAndMulti.bed.gz
247 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_reads_single.bed.gz
86 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bedgraph
210 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
91 B

PTBP1_Hela_WT_20110427_LUjh27_1

FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-1.fastq.gz
141 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-1_fastqc.zip
425.84 kB
Cutadapt (single-end)
report.txt
671 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.fastq.gz
123 B
fastqc
Directory
STAR
ptbp1-hela-wt-20110427-lujh27-1_trimmed_unmapped.out.mate1.fastq.gz
85 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam.bai
60.16 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam
3.24 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_SJ.out.tab
0 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bw
15.43 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bed.gz
103 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_singleAndMulti.bed.gz
111 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_reads_single.bed.gz
109 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bedgraph
238 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
91 B
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.tar.gz
959 B
iCount summary
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_type.tsv
109 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_subtype.tsv
79 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_gene.tsv
128 B

PTBP1_Hela_WT_20110427_LUjh27_1

FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-1.fastq.gz
157.55 MB
ptbp1-hela-wt-20110427-lujh27-1_fastqc.zip
332.89 kB
stderr.txt
1.26 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
667 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.fastq.gz
159.61 MB
iCount summary
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_subtype.tsv
1023 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_type.tsv
439 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_gene.tsv
1.61 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
255.30 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.tar.gz
1.11 MB
STAR
ptbp1-hela-wt-20110427-lujh27-1_trimmed_unmapped.out.mate1.fastq.gz
22.60 MB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam
266.62 MB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_SJ.out.tab
329.70 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_stats.txt
1.80 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam.bai
3.68 MB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_skipped.bam
3.56 kB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_reads_single.bed.gz
15.00 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_singleAndMulti.bed.gz
21.85 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bed.gz
14.87 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bedgraph
71.37 MB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome.tar.gz
466.95 kB
iCount peaks
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
1.72 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_scores.tsv.gz
11.28 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bedgraph
7.62 MB

No Sample

STAR
ptbp1-hela-wt-20110427-lujh27-3_trimmed_SJ.out.tab
193.95 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_unmapped.out.mate1.fastq.gz
11.61 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam
142.46 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam.bai
3.76 MB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_stats.txt
1.80 kB
iCount summary
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_gene.tsv
1.91 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_type.tsv
440 B
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_summary_subtype.tsv
1.01 kB
Paraclu
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_peaks.bed.gz
738.13 kB
PEKA
4mer analysis of Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.tar.gz
759.51 kB
iCount annotate
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_annotated.bedgraph
158.23 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna_annotated.bed.gz
39.63 MB
iCount group
Group_Analysis_PTBP1_Merged_Replicates_grouped_reads.bed.gz
32.90 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.bedgraph
158.23 MB
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.bed.gz
32.68 MB
iCount RNA-maps
Group_Analysis_PTBP1_Merged_Replicates_grouped_cdna.tar.gz
1.63 MB
FASTQ file (single-end)
fastqc
Directory
PTBP1_iCLIP1_data_fastqc.zip
509.12 kB
PTBP1_iCLIP1_data.fastq.gz
487.35 MB
stderr.txt
1015 B
Upload iCount sample annotation
iCLIP1_PTBP1_annotation_sheet.tab.gz
920 B
iCLIP1_PTBP1_annotation_sheet.xlsx
15.11 kB
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
436 B
FASTQ file (single-end)
stderr.txt
935 B
fastqc
Directory
demux_nomatch.fastq.gz
29.70 MB
demux_nomatch_fastqc.zip
461.37 kB
FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-noab-20110427-lujh27.fastq.gz
1.05 MB
stderr.txt
1.32 kB
ptbp1-hela-wt-noab-20110427-lujh27_fastqc.zip
354.02 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.26 kB
ptbp1-hela-wt-20110427-lujh27-2_fastqc.zip
335.50 kB
ptbp1-hela-wt-20110427-lujh27-2.fastq.gz
51.86 MB
FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-1.fastq.gz
157.55 MB
ptbp1-hela-wt-20110427-lujh27-1_fastqc.zip
332.89 kB
stderr.txt
1.26 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.26 kB
ptbp1-hela-wt-20110427-lujh27-3.fastq.gz
81.06 MB
ptbp1-hela-wt-20110427-lujh27-3_fastqc.zip
335.37 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
667 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.fastq.gz
159.61 MB
iCount summary
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_subtype.tsv
1023 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_type.tsv
439 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_gene.tsv
1.61 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
255.30 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.tar.gz
1.11 MB
FASTQ file (single-end)
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27.fastq.gz
85.32 MB
stderr.txt
1.23 kB
ptbp1-hela-wt-20110427-lujh27_fastqc.zip
335.06 kB
iCount summary
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
1016 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
431 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
1.42 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
102.78 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.tar.gz
895.61 kB
Cutadapt (single-end)
report.txt
666 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-2_trimmed.fastq.gz
52.09 MB
iCount summary
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
414 B
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
900 B
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
437.34 kB
iCount RNA-maps
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.tar.gz
414.55 kB
Paraclu
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
284 B
PEKA
4mer analysis of ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome.tar.gz
164 B
Cutadapt (single-end)
fastqc
Directory
report.txt
666 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.fastq.gz
82.24 MB
Cutadapt (single-end)
fastqc
Directory
report.txt
664 B
ptbp1-hela-wt-20110427-lujh27_trimmed.fastq.gz
86.47 MB
Cutadapt (single-end)
report.txt
669 B
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.fastq.gz
1.01 MB
fastqc
Directory
STAR
ptbp1-hela-wt-20110427-lujh27-2_trimmed_unmapped.out.mate1.fastq.gz
7.38 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bam.bai
3.69 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bam
88.86 MB
ptbp1-hela-wt-20110427-lujh27-2_trimmed_stats.txt
1.80 kB
ptbp1-hela-wt-20110427-lujh27-2_trimmed.bw
69.63 kB
ptbp1-hela-wt-20110427-lujh27-2_trimmed_SJ.out.tab
107.79 kB
STAR
ptbp1-hela-wt-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
11.36 MB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam
146.28 MB
ptbp1-hela-wt-20110427-lujh27_trimmed_SJ.out.tab
185.52 kB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam.bai
3.80 MB
ptbp1-hela-wt-20110427-lujh27_trimmed_stats.txt
1.80 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_skipped.bam
3.32 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_singleAndMulti.bed.gz
12.34 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bed.gz
8.24 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_reads_single.bed.gz
8.30 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bedgraph
38.99 MB
STAR
ptbp1-hela-wt-20110427-lujh27-1_trimmed_unmapped.out.mate1.fastq.gz
22.60 MB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam
266.62 MB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_SJ.out.tab
329.70 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_stats.txt
1.80 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam.bai
3.68 MB
iCount summary
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_type.tsv
429 B
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_gene.tsv
1.27 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_summary_subtype.tsv
1009 B
STAR
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bam.bai
1.78 MB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
152.64 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bam
2.52 MB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_SJ.out.tab
4.90 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed_stats.txt
1.79 kB
ptbp1-hela-wt-noab-20110427-lujh27_trimmed.bw
22.52 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_skipped.bam
3.24 kB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.bed.gz
5.03 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.bedgraph
23.54 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_singleAndMulti.bed.gz
7.62 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_reads_single.bed.gz
5.08 MB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_skipped.bam
3.49 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bed.gz
8.58 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
8.64 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
12.71 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bedgraph
40.72 MB
Paraclu
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bed.gz
42.18 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single.tar.gz
733.17 kB
iCount summary
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_gene.tsv
1.43 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_type.tsv
434 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_summary_subtype.tsv
1012 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
91.16 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_skipped.bam
3.56 kB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_reads_single.bed.gz
15.00 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_singleAndMulti.bed.gz
21.85 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bed.gz
14.87 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bedgraph
71.37 MB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome.tar.gz
394.24 kB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome.tar.gz
466.95 kB
iCount xlsites
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.bed.gz
113.92 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_skipped.bam
2.90 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single.bedgraph
434.49 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
215.26 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
115.58 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.tar.gz
914.72 kB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome.tar.gz
416.27 kB
PEKA
4mer analysis of ptbp1-hela-wt-20110427-lujh27_mapped_to_genome.tar.gz
439.68 kB
FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-3.fastq.gz
268 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-3_fastqc.zip
702.63 kB
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.tar.gz
959 B
FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-2.fastq.gz
37 B
iCount peaks
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bed.gz
281.20 kB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_scores.tsv.gz
4.00 MB
ptbp1-hela-wt-20110427-lujh27-2_mapped_to_genome_single_peaks.bedgraph
1.04 MB
iCount peaks
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bedgraph
2.74 MB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
677.60 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_scores.tsv.gz
6.63 MB
iCount peaks
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_scores.tsv.gz
155.82 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bedgraph
8.12 kB
ptbp1-hela-wt-noab-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
3.24 kB
iCount peaks
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
1.72 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_scores.tsv.gz
11.28 MB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bedgraph
7.62 MB
iCount peaks
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bedgraph
2.40 MB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
602.09 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_scores.tsv.gz
6.39 MB
FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27-1.fastq.gz
141 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27-1_fastqc.zip
425.84 kB
FASTQ file (CLIP)
ptbp1-hela-wt-20110427-lujh27.fastq.gz
347 B
fastqc
Directory
ptbp1-hela-wt-20110427-lujh27_fastqc.zip
696.21 kB
Paraclu
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_peaks.bed.gz
89 B
FASTQ file (CLIP)
ptbp1-hela-wt-noab-20110427-lujh27.fastq.gz
37 B
Cutadapt (single-end)
report.txt
671 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.fastq.gz
250 B
fastqc
Directory
Cutadapt (single-end)
report.txt
671 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.fastq.gz
123 B
fastqc
Directory
Cutadapt (single-end)
report.txt
668 B
ptbp1-hela-wt-20110427-lujh27_trimmed.fastq.gz
329 B
fastqc
Directory
STAR
ptbp1-hela-wt-20110427-lujh27-3_trimmed_unmapped.out.mate1.fastq.gz
204 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam.bai
6.08 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bam
3.59 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27-3_trimmed_SJ.out.tab
0 B
ptbp1-hela-wt-20110427-lujh27-3_trimmed.bw
15.54 kB
STAR
ptbp1-hela-wt-20110427-lujh27-1_trimmed_unmapped.out.mate1.fastq.gz
85 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam.bai
60.16 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bam
3.24 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27-1_trimmed_SJ.out.tab
0 B
ptbp1-hela-wt-20110427-lujh27-1_trimmed.bw
15.43 kB
STAR
ptbp1-hela-wt-20110427-lujh27_trimmed_unmapped.out.mate1.fastq.gz
83 B
ptbp1-hela-wt-20110427-lujh27_trimmed.bam.bai
126.52 kB
ptbp1-hela-wt-20110427-lujh27_trimmed.bam
3.71 kB
ptbp1-hela-wt-20110427-lujh27_trimmed_stats.txt
1.76 kB
ptbp1-hela-wt-20110427-lujh27_trimmed_SJ.out.tab
74 B
ptbp1-hela-wt-20110427-lujh27_trimmed.bw
15.51 kB
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bed.gz
80 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_singleAndMulti.bed.gz
247 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_reads_single.bed.gz
86 B
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single.bedgraph
210 B
iCount xlsites
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bed.gz
103 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_singleAndMulti.bed.gz
111 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_reads_single.bed.gz
109 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.bedgraph
238 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_peaks.bed.gz
91 B
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single.tar.gz
959 B
iCount xlsites
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_skipped.bam
3.07 kB
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bed.gz
120 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_singleAndMulti.bed.gz
250 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_reads_single.bed.gz
126 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.bedgraph
260 B
iCount RNA-maps
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single.tar.gz
957 B
Paraclu
ptbp1-hela-wt-20110427-lujh27-3_mapped_to_genome_single_peaks.bed.gz
91 B
iCount summary
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_type.tsv
109 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_subtype.tsv
79 B
ptbp1-hela-wt-20110427-lujh27-1_mapped_to_genome_single_summary_gene.tsv
128 B
iCount summary
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_type.tsv
196 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_subtype.tsv
79 B
ptbp1-hela-wt-20110427-lujh27_mapped_to_genome_single_summary_gene.tsv
292 B