ATAC-seq Adapter trimming

[LacquerHead]

Using the Nextra DNA prep kit and this for adapter trimming, wondering thoughts on length of adapter sequence and also is -q30 a bit on the high side?

cutadapt v1.3 -a CTGTCTCTTATACACATCT -q 30 --minimum-length 36 --paired-output

[GenoMax]

30 is very stringent, especially if you are aligning to a reference. Filter out Q10 or below in that case. Keep Q20 and more for de novo work.

[LacquerHead]

Great thanks figured that was a bit high.

Sequence seem ok to you? Some are using a shorter version of that.

30 is very stringent, especially if you are aligning to a reference. Filter at Q10 or below in that case. Keep Q20 and more for de novo work.

[GenoMax]

BBMap includes all commonly used adapter sequences in "adapters.fa" file in the resources folder of the software. As long as the "core" sequence is captured that should remove all adapter contamination.

Give BBDuk.sh a try as an alternative for cutadapt.