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trimgalore and cutadapt in two steps? #657
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Unfortunately, I don’t know what the |
@marcelm Thanks in advance |
If you describe what you want to do, I can try to help. You would need to state which type of data you have, which adapters you want to remove and which other processing you think should be done. |
@marcelm Thanks Marcel for your inputs in advance and for the discussion
3- remove the same primers (V3-V4; their specific sequences are attached above) if they are present within the sequenced data (I used the above cutadapt codes as the following step after trimGalore steps) |
Have a look at this section in the documentation: If I googled correctly, the V3-V4 primers target a region that is about 460 bp long, so longer than your read length. That means that you can use the somewhat simpler first command suggested in that section. In your case:
I am not 100% sure, but I think you don’t need to trim Nextera adapters at all. The adapters should only be part of the read when the sequenced fragment is shorter than the read length, but your fragments/amplicons should all be longer. You may have had some adapters in your data, but I would guess that these are from fragments that are not amplicons anyway. With the above command, any read pair that does not have one of the primer sequences is discarded, so the output should not contain any more adapters. |
Is it ok to close this issue? |
Hi team
I know that trimgalore is a wrapper around cutadapt but I want to check what I ran is considered fine
I ran trimgalore to remove adaptors and primers at 5' and 3' ends but then
I found that I need to check for primers within the sequences themselves and I found and I removed them
Things are ok that I did my analysis in that way? I don't want to reran the analysis again but I want to make sure that this is fine.
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