Question: Fastx toolkits: fastq_quality_filter does not discart any read
gravatar for DVR
5.2 years ago by
DVR20 wrote:

Hello All,

I made a quality plot and now I would like to remove reads with a quality less than 25. I ran

fastq_quality_filter -q 35 -v -i U/Seqs/R1.fastq -o U/forward_filter_35

A I got:

Quality cut-off: 25
Minimum percentage: 0
Input: 11781134 reads.
Output: 11781134 reads.
discarded 0 (0%) low-quality reads.

I try with a higher filter (-q 35) and also I had 0 reads discarded. Do anybody know what is happening?



ADD COMMENTlink modified 5.0 years ago by zorbax220 • written 5.2 years ago by DVR20

Is this Phred 60? illumina encoding? or perhaps phred 33 (in which case add -Q 33 at the end of the command line)?

ADD REPLYlink written 5.2 years ago by apelin20480
gravatar for zorbax
5.0 years ago by
zorbax220 wrote:

Is just -Q33 without space.

ADD COMMENTlink written 5.0 years ago by zorbax220
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1542 users visited in the last hour