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Did my CHIP-seq analysis right?
  1. I use Bowtie2 to get align my fastq file and get sam file.
  2. I use samtools view to separate mapped reads and unmapped reads to differenent bam file.
  3. I use picard to mark PCR duplicate.
  4. I use MACS to do peak calling.

Do you have any suggestion?

Thanks!

chip-seq
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written by mikysyc2016 mikysyc2016

3 answers

why do you think you need suggestions? what do you think could be improved?

based on the terse description nothing seems out of the ordinary although I don't think there's an "analysis" component yet to the ChIP-seq data processing you've described.

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written by Friederike Friederike

Before peak calling, I would also recommend removal of blacklisted regions.

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written by EagleEye EagleEye

Thanks. What knid of software and command i can use to remove them? Can I remove them after I use picard.jar to mark pcr duplicates?

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written by mikysyc2016 mikysyc2016 
bedtools intersect -abam sample_sorted.bam -b blacklist.bed -v > sample_sorted_blacklistRemoved.bam

You can do it at any step after alignment.

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written by EagleEye EagleEye

Please do not post comments as answers. When replying to a specific answer or comment, use the ADD COMMENT bellow said comment or answer.

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written by h.mon h.mon

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