TrimGalore parameter form Nextera paired-end reads adapter removal
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4.8 years ago
gundalav ▴ 360

I have Nextera data, according to the document, the adapter is this:

enter image description here

My question is what's the right parameter to use for trim_galore?

Does this command suffice?

trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired --nextera  -o $TRIMGALORE_DIR $READ1 $READ2

I prefer to use -a and -a2 parameter, but not sure how to do it.

adapter sequencing illumina trimming nextera • 3.7k views
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4.8 years ago

Just use the --nextera flag. If you insisted on setting -a, then both it and -a2 should be CTGTCTCTTATA, which is the reverse-complemented start of the adapters.

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Hi Devon,

Thanks for the reply:

Do you mean this command?

trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired -a CTGTCTCTTATA  -a2 CTGTCTCTTATA  -o $TRIMGALORE_DIR $READ1 $READ2
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Yes, something like that should work.

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