Question: R reads q-score
0
gravatar for Manuel Mendoza
2.6 years ago by
University of Vigo, Spain
Manuel Mendoza0 wrote:

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.

rna-seq • 977 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 2.6 years ago by Manuel Mendoza0
3

the read q-score

What's that?

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster41k

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

ADD REPLYlink written 2.6 years ago by Manuel Mendoza0

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

helps to filter the reads by quality score.

ADD REPLYlink modified 16 months ago • written 16 months ago by cpad011212k
0
gravatar for vivekbhr
2.6 years ago by
vivekbhr530
Germany
vivekbhr530 wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by vivekbhr530

Thanks you! I'm going to try it

ADD REPLYlink written 2.6 years ago by Manuel Mendoza0
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