Issues producing an output file when using fastx quality stats program

Question

[nlh15]

Hello,

I am trying to run some files through the fastx statistics program via the command

fastx_quality_stats -Q30 -i 3237-WHJ-0001_S1_L001_R1_001.fastq \ -o 3237-WHJ-0001_S1_L001_R1_001.stats

The quality check works fine but it doesnt produce an output file, just spills the info out in the terminal.

How can I produce an output file for later use?

Appreciate any wisdom!

// Nine

Answer 1

[GouthamAtla]

You should remove the \ from your command. Are you sure the offset is 30?

fastx_quality_stats -Q30 -i 3237-WHJ-0001_S1_L001_R1_001.fastq -o 3237-WHJ-0001_S1_L001_R1_001.stats

[nlh15]

Thank you that did it. Doing some experiments on some data but I will most likely go back to the standard Q33