View Single Post
Old 08-20-2014, 12:37 AM   #26
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707


For the "ref=" flag, the adapters should be in fasta format. To use the "literal=" flag, you don't need to put them in a file. I'm not sure what the "P-" prefix signifies on the first adapter, but the way you would trim PE reads with those sequences is like this: -Xmx1g in1=read1.fq in2=read2.fq out1=trimmed1.fq out2=trimmed2.fq k=28 mink=13 hdist=1 ktrim=r literal=GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG,ACACTCTTTCCCTACACGACGCTCTTCCGATCT tpe tbo

(all one line)

5' adapters will end up being seen on the 3' (right) end of the reads when the insert size is too short, so for that, you use the "ktrim=r" flag (meaning when a kmer matches the reference, trim that kmer and everything to the right).

I also included a file "truseq.fa.gz" in the /resources/ directory which contains the most commonly-used Illumina adapter sequences, though the ones you mention are not in it.

P.S. I added the "tpe" (trim pairs equally) and "tbo" (trim by overlap) flags. These improve the sensitivity for paired-end fragment libraries, in which the adapter should occur in the same place on each read and reads with adapter sequences should overlap when reverse-complemented. Adapter-trimming is actually possible using these flags only, without even specifying the sequences to trim, but the highest efficiency is attained by doing both overlap and sequence trimming. These flags should NOT be used with long-mate-pair libraries, and have no effect on single-ended libraries.

Last edited by Brian Bushnell; 08-20-2014 at 10:08 AM.
Brian Bushnell is offline   Reply With Quote