Did my CHIP-seq analysis right?

Question

[mikysyc2016]

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!

Answer 1

[Friederike]

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.

Answer 2

[EagleEye]

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

Answer 3

[mikysyc2016]

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?

[EagleEye]

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

You can do it at any step after alignment.

[h.mon]

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