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No trimming when no adapter is found #64
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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 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. |
Thanks for the fast reply. I would be very happy with the solution you propose, and leaving the 'thresholding problem' to me/the user. |
Alright, let me see what I can do (probably tomorrow though). |
No hurries, thanks a lot! |
Sorry for being not entirely truthful, I have now tried to add the option A description should come up with |
Can't complain! Thanks a lot |
p.s. any idea when this will be 'released'? |
Thanks for the feedback. Given that there are some four changes already I suppose we could make a release soon. Let me just grab a coffee... |
Here we go, v0.6.4 has just been posted. Enjoy! https://github.com/FelixKrueger/TrimGalore/releases/tag/0.6.4 |
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)
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