R reads q-score

Question

[Manuel Mendoza]

Hello,

I want to calculate the read q-score (one per one) in a fastq file. Does anyone know any R package to do it?

I am working with RNA-seq data and I want to trim the read data (Read q-score>30). How can i do that using R? I don't want to use python.

Thanks you.

[WouterDeCoster]

the read q-score

What's that?

And why is "proteomics" a logical tag for your question?

[Manuel Mendoza]

because i want to assemble the proteome after clean up my data

[cpad0112]

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_quality_filter_usage

helps to filter the reads by quality score.

Answer 1

[vivekbhr]

The ShortRead package in bioconductor is what you are looking for..

[Manuel Mendoza]

Thanks you! I'm going to try it