Question: R reads q-score
0
gravatar for Manuel Mendoza
3.9 years ago by
University of Vigo, Spain
Manuel Mendoza10 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 • 1.4k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 3.9 years ago by Manuel Mendoza10
3

the read q-score

What's that?

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

ADD REPLYlink written 3.9 years ago by WouterDeCoster45k

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

ADD REPLYlink written 3.9 years ago by Manuel Mendoza10

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

helps to filter the reads by quality score.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by cpad011215k
0
gravatar for vivekbhr
3.9 years ago by
vivekbhr630
Germany
vivekbhr630 wrote:

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

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by vivekbhr630

Thanks you! I'm going to try it

ADD REPLYlink written 3.9 years ago by Manuel Mendoza10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1010 users visited in the last hour
_