Trouble with transcriptome data

Question

[gayachit]

Hi everyone

I have 14 Gb of transcriptome data of a plant sequences using Ion Proton. Initially I ran a quality assessment tool for checking it and there are a lot of overrepresented sequence probably rRNA. When I try to use fastq_quality_filter to remove low quality bases it gives me an error "Invalid quality score on line 210650840 [quality tok >:::;998;;::;5;;5<<18:;<<<=?7<;;;;;;<<==?;;;5;;299;::"

I tried searching for similar posts. Now m thinking whether to remove the whole read or not. Please suggest what can be done

[WouterDeCoster]

Please chose a more informative title and add relevant tags, such as ion proton

Answer 1

[gangireddy]

Hi gayachit,

This is a naive answer. But here it goes :

It will not affect your data if remove a single read.

and generally the first few bases of most sequencing reads have poor qualities and they need to be chopped off.

so, you can try chopping of first few bases.

[gayachit]

Thanks gangreddy Those bases were at the end of my file. So i removed them

Answer 2

[Benn]

You'll probably have to set the phred score parameter to -Q33.

[gayachit]

-Q33 didn't work. I tried that earlier... But thanks anyway

[Benn]

Okay, it would be helpful if you explained already what you have tried. Or present some code, just an idea.