Just for ask, have the bug highlighted in this thread Cutadapt thinks my fastq.gz files aren't fastq.gz been solved? I met a same bug
missing sequence for record beginning on line 5
, and trim the primer one-by-one seems a little annoying because I have 30*2(illumina paired) files… Thanks!
Hi there @wym199633, unfortunately that bug hasn’t been fixed yet. You can try the workaround I posted further down in the thread you linked to. Please let us know if you get stuck or need assistance, we are here to help!
For the paired-end reads, I did
cutadapt --front forwardprimer -m 1 SRRxxxxx_1.fastq.gz -o trimmed/SRRxxxxx_1.fastq.gz
cutadapt --adapter reverseprimer -m 1 SRRxxxxx_2.fastq.gz -o trimmed/SRRxxxxx_2.fastq.gz
Is this the right way to trimming primers off?
That’s close, but the
--adapter options have more to do with which end of the DNA you are operating on.
This section of the cutadapt docs helps explain it a bit better. The
-g flag is also called
--front and the
-a flag is also called
--adapter. So you’d want to use the
-g flag with your forward primer on your forward read and also use a reverse-complemented reverse-primer with the
-a flag on your forward read to drop the reverse primer (only needed if your amplicon is short enough that this is a concern, e.g. ITS).
Then on your reverse reads same deal, but now you are using the normal reverse primer with
-g and the reverse complemented forward primer with
Basically you are always going to use
--front even on your reverse reads, but you may also need
--adapter if you might have sequenced over your reverse primer.
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