Question: fastx_collapser: Invalid quality score value (char '/' ord 47 quality value -17). Why?
0
gravatar for jaqx008
4 months ago by
jaqx00840
jaqx00840 wrote:

Hey everyone, I am currently trying to use fastx_collapser of a fastq file and I am getting the error below. When I looked in the fastq file, there are numerous places with '/'. How do I correct this and collaps my fastq file? By the way, I have tried some of the recommendations with -Q33 and out put file wasnt a fastq file and dont know what to do with it. Thanks

fastx_collapser -v -i file.fastq -o 2file.fastq

fastx_collapser: Invalid quality score value (char '/' ord 47 quality value -17) on line 56

AAAAAEEEAEEAAEAEE/EAE/EEEEEAEEE/E/EE
@NS500519:44:HHHTLBGX2:1:11101:23901:1069 1:N:0:CAGATC
GTAACCTGTAGATCCGAATTTGTG
+ 
6A6/AE/AE6EE/EEEAA6EE/EE 
@NS500519:44:HHHTLBGX2:1:11101:5260:1069 1:N:0:CAGATC 
CATTGCACTCGTCCCGGCCTGA
ADD COMMENTlink modified 4 months ago • written 4 months ago by jaqx00840

/ is a valid quality character for Phred+33.

Is the fastq snippet you posted the very beginning of the file? Because it starts at a quality line, not at a header. Mind you, there is a previous post where the error has been exactly this: FASTX error - quality score

ADD REPLYlink modified 4 months ago • written 4 months ago by h.mon21k

No its not the begining of the file. its somewhere after line 50 I think.

ADD REPLYlink written 4 months ago by jaqx00840

Ok let me try this suggestions.

ADD REPLYlink written 4 months ago by jaqx00840
0
gravatar for swbarnes2
4 months ago by
swbarnes24.5k
United States
swbarnes24.5k wrote:

Well, the stupid easy way to deal with this...use sed to change all the "/" to a legal quality character.

ADD COMMENTlink written 4 months ago by swbarnes24.5k
0
gravatar for genomax
4 months ago by
genomax59k
United States
genomax59k wrote:

I suggest that you use clumpify.sh ( A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files ) instead of fastx_collpaser.

ADD COMMENTlink modified 4 months ago • written 4 months ago by genomax59k
0
gravatar for Philipp Bayer
4 months ago by
Philipp Bayer5.8k
Australia/Perth/UWA
Philipp Bayer5.8k wrote:

Another suggestion:

Run Trimmomatic on your data with the TOPHRED33 flag, see whether that'll change your quality scores.

ADD COMMENTlink written 4 months ago by Philipp Bayer5.8k
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