TrimGalore parameter form Nextera paired-end reads adapter removal

Question

[gundalav]

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

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.

[Brian Bushnell]

See also this thread:

Why mapping rate is low after adapter trimming paired-end data?

Answer 1

[Devon Ryan]

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.

[gundalav]

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

[Devon Ryan]

Yes, something like that should work.