Fastx quality filtering error

Question

[athira112athira]

Hi,

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?

[ATpoint]

Output of head -n 4 sra_data.fastq ?

[athira112athira]

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  
CGCAACATTACCGCGGCTGCTGGCACGTAGTTAGCCGTCCTCTTGGTAAGATACCGTCACAGTGTGAACTTTCCACTCTCACACTCATTCTTCTCTTACAACAGAGCTTTACGATCCGAAACCTTCTTCACTCACGCGGCGTTGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCCTAGGTCGGCTATGTATCGTCGCCTTGGTGAGCCGTTACCCCACCAACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAATTGCCACCTTTAAGTAAATGTCATGCAACATCTACTATTATGCGGTATTAGCTATCGTTTCCAATAGTTATCCCGCCGTACCAGGCAGGTTACCTACGCGTTACTCACCCGTTCGCAACTCATCCAGAGAAGCAAGCTCCTCCTTCAGCGTTCTACTTGCATGTATTAGGCACGCCGCCAGCGTT
+SRR6031690.1.1 I2SY8KZ01A1O0T length=510
IIIIIHHIIIHHD888;FH@===IIIIIH@@@CDIIII544===>>>;;;>HADDEIIIIIIIIIIIII88888GFFFHIIIIIIIIIIIIIIIIEEEHIIIIIIHIHHAA@A@?@@@12266IHHFFHHIIIIIIIIIIIIIIIIIIIIIIIIHHHHHHF::;;;EHEGHHGHHH777CDF@@666>96111CCC@@@CE=:;;CCHFFFFCCA=;222?AFCF???>?>>>>A9;6666;666>BEEHFHEEGIIIIHIEEEEHHHHD@@@FEE@@@DFFHHHHHHHHHHEEEFFFFFFFFHHHFEEEEIIHHHEEEHDB=<;@=944465...77?=//06<BEHHHHHHHHHHHHEEEFFHFE>>>HHDDEHHHHH@:555FDCBB????72---0///000017===>>CDEDFEHA??>DDCC@@@CCCDHHHHHHHHHHHC@===?DD@AB@EDB===>?EDDEHHIDC>==DHHHECCBCCDCA@888<@<:9;555;=?..

[Bastien Hervé]

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!

[athira112athira]

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

Answer 1

[ATpoint]

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.

[athira112athira]

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