Skip to content

Changed adapter trimming parameters to fix overtrimming issues

BIOPZ-Katsantoni Maria requested to merge adapter_ovetrimming into master

Closes issue #92 Changed the pair-filter=any as suggested and changed some more parameters that possibly led to overtrimming, namely:

  • the --n option was too high. We need this to be 2 only when trimming adapters to cover for the case when we have two adapters in one read. For the poly-A it leads to overtrimming of A stretches

  • I removed the --match-read-wildcards option. Not sure what it does. It was present only in some of the cut adapt commands.

  • -q 6 when trimming poly-As might lead again to overtrimming so I removed it

  • the -O 1 is there if we want to be super strict (for now I left it and added it to both paired-end and single-end)

In general fixed so that there is an agreement of those parameters between single-end and paired-end where there were inconsistencies

Edited by BIOPZ-Katsantoni Maria

Merge request reports