job submission command

[LiangMa2017]

Hi Jin, I have 2 tested files ran successfully, the command I used is as below. N2 results look weird as shown in washU browser. I guess my command is not right. What do you think? And I'm not sure the controls are needed, we don't have controls.

N1: single-end with replicates and controls

bds_scr h3k27ac_noncellcycle_dmso20180519 ~/TF_chipseq_pipeline/chipseq.bds -q chettys -se -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out20180519 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz -fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4 Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz

N2: paired-end without replicates and controls

bds_scr SRR3554631 ~/TF_chipseq_pipeline/chipseq.bds -q chettys -pe -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out -fastq1_1 SRR3554631_1.fastq.gz -fastq1_2 SRR3554631_2.fastq.gz

bigwig files

N1: out20180519/signal/macs2/pooled_rep/ N2: out/signal/macs2/rep1/

[leepc12]

Your command for the case 2) looks good. Having a control set is recommended but not required.

[LiangMa2017]

Sounds great. Thank you.