Any pitfalls to consider when using MACS on paired-end data when forward and reverse reads are different lengths?
I have some paired-end data where the forward and reverse reads are different lengths (due to unrelated requirements of someone else's samples on a multiplexed sequencing run).
Can I use the entirety of both reads when I predict peaks with MACS2 or should I trim the longer reverse reads? Are there any parameters that should change to account for the different read lengths?
Are there any potential problems from using the different length forward/reverse reads?
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