Question: Fastx quality filtering error
0
gravatar for athira112athira
16 months ago by
athira112athira10 wrote:

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?

fastx software error • 461 views
ADD COMMENTlink modified 16 months ago by finswimmer13k • written 16 months ago by athira112athira10

Output of head -n 4 sra_data.fastq ?

ADD REPLYlink written 16 months ago by ATpoint34k

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;=?..
ADD REPLYlink modified 16 months ago by Bastien Hervé4.5k • written 16 months ago by athira112athira10

Hello athira112athira,

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

Thank you!

ADD REPLYlink written 16 months ago by Bastien Hervé4.5k

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

ADD REPLYlink written 16 months ago by athira112athira10
0
gravatar for ATpoint
16 months ago by
ATpoint34k
Germany
ATpoint34k 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 16 months ago by ATpoint34k

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

ADD REPLYlink written 16 months ago by athira112athira10
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