Question: Fastx toolkits: fastq_quality_filter does not discart any read
1
gravatar for DVR
5.2 years ago by
DVR20
Mexico
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?

Thanks!

 

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
0
gravatar for zorbax
5.0 years ago by
zorbax220
Mexico
zorbax220 wrote:

Is just -Q33 without space.

ADD COMMENTlink written 5.0 years ago by zorbax220
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