[BioC] Amplicon and exon level read counts and GC content
Michael Love
love at molgen.mpg.de
Wed May 30 12:23:51 CEST 2012
hi Yu Chuan,
I wrote two convenience functions, countBamInGRanges and getGCcontent, for the
exomeCopy package for these tasks. You can take a look at the first part of th
e vignette here:
[1]http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html
best,
Mike
Date: Tue, 29 May 2012 22:17:29 -0700 (PDT)
From: Yu Chuan Tai [2]<yuchuan at stat.berkeley.edu>
To: [3]bioconductor at r-project.org
Subject: [BioC] Amplicon and exon level read counts and GC content
Message-ID: [4]<alpine.DEB.2.00.1205292216070.8774 at arwen.Berkeley.EDU>
Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
Hi,
I have some questions about DNA-Seq and RNA-Seq analyses. In Amplicon
sequencing, is there any package/function which can extract amplicon-level
read counts and GC content from an aligned file of BAM format? The same
question to exon-level read counts and GC content. More generally, given a
genomic interval, how could I extract the read count and GC content for
that interval?
Thanks for any input!
Best,
Yu Chuan
References
1. http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html
2. mailto:yuchuan at stat.berkeley.edu
3. mailto:bioconductor at r-project.org
4. mailto:alpine.DEB.2.00.1205292216070.8774 at arwen.Berkeley.EDU
More information about the Bioconductor
mailing list