Question: TrimGalore parameter form Nextera paired-end reads adapter removal
1
gravatar for gundalav
2.8 years ago by
gundalav290
La La Land
gundalav290 wrote:

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.

ADD COMMENTlink modified 2.8 years ago by Devon Ryan93k • written 2.8 years ago by gundalav290

See also this thread:

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

ADD REPLYlink written 2.8 years ago by Brian Bushnell17k
1
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Devon Ryan93k

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
ADD REPLYlink written 2.8 years ago by gundalav290
1

Yes, something like that should work.

ADD REPLYlink written 2.8 years ago by Devon Ryan93k
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