Ran a ChIP-seq experiment with cells treated with vehicle and a drug, so sequenced 4 samples (vehicle input, vehicleIP, drugInput, drugIP). During multiplexing the vehicle input was unevenly added to the pooled libraries, and following sequencing therefore had a much bigger fastq file. I am wondering about usability of these results and how to potentially adjust during analysis for this uneven loading. Thank you.
p.s. The 3 smaller fastq files still gave a good amount of aligned reads so thats not an issue. Just thinking in terms of peak calling, differential peak analysis etc.
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written
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rbronste
1 answer
Just downsampling the big fastq might be a good plan. You can use samtools for this. I'd visualize all the results too before analysis.
I find Chip-seq to be notoriously dodgy.
Yep, sounds about right!
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