This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Unexpected small reads ATAC-seq

Hello all,

I am processing the original ATAC-seq dataset from Buenrostro et al. 2013. After removing the adapters with cutadapt, where I set a minimum fragment size of 20, and mapping, I filter all the reads shorter than 40 bp to avoid those that only contain adapter. Surprisingly, in the insert size plot, I still see a tiny fraction of very short reads. How is this possible? Is this normal?

Thanks in advance

enter image description here

atac-seq
• 745 views • link
updated by Ram Ram • written by gen23crassus • gen23crassus

1 answer

It is probably reads from the mitochondrial genome that are so chopped down and overdigested that you get these small fragments, or some weirdness from the aligner. I say it in that sloppy fashion because it is so few reads that it essentially does not matter. The plot overall looks perfectly normal for this type of experiment, so carry on.

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this