Quality plots of NextSeq data

BBMap short read aligner, and other bioinformatic tools.

Brought to you by: brian-jgi

Quality plots of NextSeq data

Forum: General Discussion

Creator: Lavinia Gordon

Created: 2015-03-03

Updated: 2015-03-03

Lavinia Gordon - 2015-03-03

Hi Brian,

I am trying to replicate your plots as discussed on seqanswers - http://seqanswers.com/forums/showthread.php?t=40741

bbduk.sh in=reads.fastq.gz out=trimmed.fq.gz ktrim=r k=23 hdist=1 mink=11 tpe tbo minlen=90 ref=truseq.fa.gz,nextera.fa.gz

bbmap.sh maxindel=200 in=trimmed.fq.gz mhist=mhist.txt bhist=bhist.txt qhist=qhist.txt qahist=qahist.txt

Can I just confirm that truseq.fa.gz and nextera.fa.gz are just the gzipped adapter sequences in FASTA format?

Many thanks.

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Lavinia Gordon - 2015-03-03

Ah, ignore this, just found them :)
bbmap/resources
thanks!

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Log in to post a comment.