eCLIP-seq differential peak¶
Summary¶
This pipeline is based on the input normalization code from ENCODE.
Input normalization: Compares the number of reads within the IP sample to the number of reads within the size-matched INPUT sample across Clipper-called peak clusters
Input¶
3 input files. User should run this pipeline inside the eCLIP-seq jobID folder.
WT sample
KO sample
Input sample
Usage¶
hpcf_interactive.sh # login to compute node
module load conda3/202011
source activate /home/yli11/.conda/envs/captureC
module load perl
eclip_diff_peak.py $wt $ko $input
# stderr
Input is: 2472461_Nontarget_cd34_10_IP_S5_R1 2472462_M1_3_cd34_10_IP_S6_R1 2472458_Nontarget_cd34_10_Input_S2_R1
reading peak file 2472461_Nontarget_cd34_10_IP_S5_R1_results/2472461_Nontarget_cd34_10_IP_S5_R1.bed
now doing expt 2472461_Nontarget_cd34_10_IP_S5_R1.pri.bam
now doing input 2472458_Nontarget_cd34_10_Input_S2_R1.pri.bam
CLOSE
(in cleanup) Internal error: could not get STATE from IPC::Run
(1702, 6)
reading peak file 2472461_Nontarget_cd34_10_IP_S5_R1.enriched_peak.bed
now doing expt 2472461_Nontarget_cd34_10_IP_S5_R1.pri.bam
now doing input 2472462_M1_3_cd34_10_IP_S6_R1.pri.bam
CLOSE
(in cleanup) Internal error: could not get STATE from IPC::Run
(424, 6)
Output¶
Please see the *enriched_peak.final.bed file. The 4th and 5th columns are -log10 pvalue and logFC.