Question: Fastx quality filtering error
gravatar for athira112athira
4 months ago by
athira112athira0 wrote:


I use fast-x toolkit for quality filtering of my data. I get an error when running the command

fastq_quality_filter -v -Q 64 -q 25 -p 75 -i sra_data.fastq -o sample_filtered.fastq
fastq_quality_filter: Invalid quality score value (char '.' ord 46 quality value -18) on line 4

I need a moderate threshold of average quality>25. please, can anyone suggest a possible solution for this?

fastx software error • 189 views
ADD COMMENTlink modified 4 months ago by finswimmer11k • written 4 months ago by athira112athira0

Output of head -n 4 sra_data.fastq ?

ADD REPLYlink written 4 months ago by ATpoint17k

This is the output for head -n 4 sra_data.fastq

dcb@dcb-P6-2355IL:~$ head -n 4 sra_data.fastq

@SRR6031690.1.1 I2SY8KZ01A1O0T length=510  
+SRR6031690.1.1 I2SY8KZ01A1O0T length=510
ADD REPLYlink modified 4 months ago by Bastien Hervé4.3k • written 4 months ago by athira112athira0

Hello athira112athira,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

ADD REPLYlink written 4 months ago by Bastien Hervé4.3k

Thank you so much, I will take care about it from the very next post.

ADD REPLYlink written 4 months ago by athira112athira0
gravatar for ATpoint
4 months ago by
ATpoint17k wrote:

Looks like a normal fastq file. In any case, I recommend going away from fastx-toolkit. It is very old and newer (and faster) alternatives exist. Options are among others: fastp, skewer, cutadapt etc. I checked with skewer and it does not throw any error. Check which tools you feel comfortable with, they all have a lot of options to customize the trimming.

ADD COMMENTlink written 4 months ago by ATpoint17k

Thank you for your suggestion. I will try anyone of it as possible.

ADD REPLYlink written 4 months ago by athira112athira0
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