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Dear Community,
please help me, I am very frustrated with the analysis of ChIP-seq data. Could you please check if I have forgotten something in the workflow with MACS?
1) QC of FastQ
2) Alignment (e.g. BWA) and conversion to bam
3) removing unaligned reads (SAMTOOLS) and scale sample reads number down to IgG reads number (Picardtools)
4) Peak calling with MACS - PeakSplitter option enabled
macs14 -t sample.bam -c IgGcontrol.bam -n sample -f BAM -g hs --bw 200 -w --call-subpeaks
Would that be right? Although we have ~ 36 million reads, the FDR of the MACS peaks always shows 100%, I thought I might forgot a step or something.
Thank you very much.
please help me, I am very frustrated with the analysis of ChIP-seq data. Could you please check if I have forgotten something in the workflow with MACS?
1) QC of FastQ
2) Alignment (e.g. BWA) and conversion to bam
3) removing unaligned reads (SAMTOOLS) and scale sample reads number down to IgG reads number (Picardtools)
4) Peak calling with MACS - PeakSplitter option enabled
macs14 -t sample.bam -c IgGcontrol.bam -n sample -f BAM -g hs --bw 200 -w --call-subpeaks
Would that be right? Although we have ~ 36 million reads, the FDR of the MACS peaks always shows 100%, I thought I might forgot a step or something.
Thank you very much.
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