IDR peak for eCLIP-seq¶

Summary¶

Pipeline adopted from https://github.com/YeoLab/merge_peaks

bam should be R1 reads.

Input¶

input.tsv¶

7 columns tsv.

Rep1 bam, and clipper peak

Rep2 bam, and clipper peak

Input 1 and Input 2 bam file, can be the same

last column is sample label

MBNL1_IP_1_S36.dedup.bam        MBNL1_IP_1_S36.dedup.clipper.default.bed        MBNL1_IP_2_S37.dedup.bam        MBNL1_IP_2_S37.dedup.clipper.default.bed        3162889_Hudep2_Input_S27.dedup.bam      3162889_Hudep2_Input_S27.dedup.bam      Hudep2_eclip

Usage¶

hpcf_interactive

module load python/2.7.13

run_lsf.py -f input.tsv -p eclip_idr -g hg19

run_lsf.py -f input.tsv -p eclip_idr -g mm10

Output¶

1. pyGREAT html report¶

Please check your email for link.

2. peak annotation¶

idr_peaks.rmblck.homer.annotated.tsv

3. annotation pie chart¶

A simplified pie chart where priority is Exon,Promoter,5UTR,3UTR,Intron,Intergenic

4. homer motif discovery (top 1k peaks used)¶

default parameter output: homer_motifs_result
short motif output: homer_motifs_result_short

TODO¶

https://github.com/YeoLab/rbp-maps https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md https://rnaseq-mats.sourceforge.io/

create a figure similar to fig 5: https://www.nature.com/articles/s41586-020-2077-3#MOESM1

code @ github.