Question: bbduk: quality filtering and singletons
0
gravatar for rororo
14 months ago by
rororo0
rororo0 wrote:

I want to use bbduk of the bbmap package to quality filter my paired-end Illumina reads according to the following:

  • minimum quality value of 2
  • minimum length of 36
  • remove single reads

To me, the bbduk manual is here a bit unclear. Does the following command remove singletons?

bbduk.sh in1=R1.fq in2=R2.fq out1=R1.clean.fq out2=R2.clean.fq trimq=2 minlen=36
bbmap reads genome • 478 views
ADD COMMENTlink written 14 months ago by rororo0
1
gravatar for genomax
14 months ago by
genomax64k
United States
genomax64k wrote:

If by singletons you mean removal of a read from R1, if the corresponding read from R2 was discarded, then yes. Trimming paired-end reads together keeps the reads in sync in both files.

Note: There is another tool called repair.sh that can fix files that you may receive that have reads out-of-sync.

ADD COMMENTlink modified 14 months ago • written 14 months ago by genomax64k

this, plus if there is a read present in R1 but the corresponding one is missing in R2

ADD REPLYlink written 14 months ago by rororo0

See my edit to the post above. It will not happen as a part of bbduk.sh run.

ADD REPLYlink written 14 months ago by genomax64k
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