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  • Chip-seq tags of unequal length - is this a problem for macs?

    I have a chip-seq sample where a significant proportion of the reads have low quality bases at the end. Trimming these bases using sickle or Trimmomatic produces reads of unequal length. Is this a problem for macs? I see that one of the first things macs does is to estimate the tag size based on the first 10 tags in the sample which may - or may not - be representative. Is macs assuming equal length for all tags?

  • #2
    No, it is not a problem. It is used to check if the estimated fragment length differs from the read length.

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