What is the best way to find broad ChIP-Seq peaks using a BAM file with 600 million reads?
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4.6 years ago
biorepine ★ 1.5k

Dear Biostars,

I generally use MACS program to identify broad peaks directly from a BAM file (without worrying about converting BAM into something else). However, it is still time consuming when I run it on a file with many sequencing reads (in my case 600 million reads). Is there any faster approach to do this ?

thanks in advance.

ChIP-Seq MACS • 1.2k views
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