bbduk: quality filtering and singletons
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
1 answer
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.
Log in to answer this question.
More posts like this
-
How to trim bases with bbduk.sh
written by shivangi.agarwal800
-
MultiQC output shows that data processing steps are ineffective
written by melissachua90 •
-
BBDuk returned java.lang.AssertionError
written by melissachua90 •
-
BBDuk quality filtering not producing expected results
written by rebeliscu •
-
bbduk can't read file
written by Frank •
-
Read detection with pattern in paired end FASTQ file
written by amitpande74 •
-
Java error message when using BBDuk
written by c.e.chong •
-
BBDuk output different sized paired end reads
written by GLFrey •
-
Bulk quality filtering with bbduk
written by Felix_1993 •
-
BBDuk trimming concern: large discarded, too aggressive (?)
written by umn_bist •
