Fastx quality filter

Question

[kriti.awasthi23]

I am using Fastx tool to quality filter my data. The command I'm using is given below-

fastq_quality_filter -v -q 20 -p 70 -i /home/desktop/folder_name/2_R1.fastq/ /home/desktop/folder_name/2_R2.fastq -o /home/Desktop/folder_name/tomato2.txt

What parameters should I choose, and where am I going wrong? I'm not able to configure.

This is the error I'm getting-

/var/spool/PBS/mom_priv/jobs/183464.login1.SC: line 14: module: command not found
/var/spool/PBS/mom_priv/jobs/183464.login1.SC: line 16: fastq_quality_filter: command not found

Please help me with this. Thanks in advance!

[GenoMax]

You may be better off not using Fastx toolkit. You would minimally need to add -Q 33 to indicate sanger format fastq data (which is needed for Fastx-tookit tools and recent data).

[Dan D]

Agreed. A better tool for quality trimming is sickle.

[Medhat]

what parameters i should choose

you are running the command or you are asking us to tell you the command?

did you read the manual?
FASTQ Quality Filter

[kriti.awasthi23]

yes i did read the manual....and m asking if m going the rught way thn what is d problem.

[Ram]

yes i did read the manual....and m asking if m going the rught way thn what is d problem.

This is what that should be: "Yes I did read the manual, and I'm asking if I'm going the right way, then what's the problem."

Please write as a professional would.

[Medhat]

yes you are doing good (I understood after @Ram explanation), The command should work good and as you know from the manual you asking to have 70% of the read have quality of 20 (If you are asking is this parameters are good or I need to change it? it depends on what the question you are asking or getting from data)

[Ram]

Why do you think you're going "wrong"? Does your command fail? If so, what's the error message? Do you not get the output that you should be getting? If so, what's the difference between the expected and actual output?

Please be as detailed as you can when you ask a question. Also, please proof read. I know using m as a stand in for I'm is a thing with my compatriots, but please avoid such usage.

[Medhat]

m , d and thn

for me is not clear by the way :D

[kriti.awasthi23]

thankyou for your kind words sir, i will avoid such usage in future......the error I am getting is some module loading problem. I dont know how to resolve that!

[Medhat]

can you write the error you have?

[Ram]

Please edit your question and add the exact error message. Most module problems are seen in either python scripts with dependencies not loaded in yet, or on weirdly configured HPC environments. Unless people see the exact error message, they cannot teach you how to diagnose errors.

[kriti.awasthi23]

this is the error m getting-

/var/spool/PBS/mom_priv/jobs/183464.login1.SC: line 14: module: command not found /var/spool/PBS/mom_priv/jobs/183464.login1.SC: line 16: fastq_quality_filter: command not found

[Medhat]

try this before calling the modules

. /etc/profile.d/env-modules.sh  
. /etc/profile.d/modules.sh

[Ram]

Why did you add this as an answer? This should be added to your original question by editing the question. I'm making the necessary changes now.

And once again, please write professionally.

[GenoMax]

Assuming "modules" system is being used to manage software on this cluster the correct command would be module load name_of_fastx_tookit_module. The name_of_fastx_tookit_module needs to be whatever it is on your cluster. You can take a look at available modules on your cluster by doing module avail.