FelixKrueger
commented
5 years ago Hi Maarten,
I am afraid as it stands Trim Galore is not set up towards not trimming at all.
One option would of course be do the checking externally, e.g. I believe FastQC writes out a table with the counts for the Illumina, Nextera and small RNA adapters anyway, so one could in theory read that and base the trimming/no trimming decision on that.
We could of course add an option that skips the adapter trimming (or sets -a X itself) if really absolutely no adapter is found. The question would then be though: Where do you draw the line? At really 0 / 0 / 0 counts for all three adapters? What happens if there is 1 count for one of them? Just to remind you, the auto-detection works on the first 1 million sequences, and the adapter sequences as 12-13bp long, so very occasionally you might find one of the sequences in a read by chance, or if it occurs in the genome somewhere....
I could of course leave that thresholding problem up to you by adding an integer threshold count that you need to set yourself (anything between 0 and ?), e.g. --consider_already_trimmed [INT]. Is that something that would help in case?
Maarten-vd-Sande
When no adapter is found, trim galore defaults to the illumina sequence and tries to remove this.
I have a pipeline that cuts automatically using trimgalore, however sometimes people send me data that is already trimmed. Since I do not want to make assumptions about whether the data is trimmed or not, I still run it through trimgalore. I was wondering if there is some option I failed to find, that if no adapter is found, quality control is performed but no adapter trimming.
I am trying to avoid manually checking if adapters exist and adding -a -X (#51)