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TrimGalore parameter form Nextera paired-end reads adapter removal

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
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updated by Devon Ryan Devon Ryan • written by gundalav gundalav

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

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
• 0 views • link
written by gundalav gundalav

Yes, something like that should work.

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written by Devon Ryan Devon Ryan

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