How I can extract the sequences of short reads mapped to a particular gene in genome in RNA-Seq
1
0
Entering edit mode
6.3 years ago
ebrahimiet ▴ 50

Hi all, I have done mapping by CLC Genomics. How I can extract the sequences of short reads mapped to a particular gene in genome in RNA-Seq?

RNA-Seq • 1.9k views
ADD COMMENT
0
Entering edit mode

pysam is a great way to work with bam files if you are familiar with python. (http://bioconductor.org/packages/release/bioc/vignettes/SNPRelate/inst/doc/SNPRelateTutorial.html). You can also use samtools view to specify the region you want to extract reads from.

ADD REPLY
1
Entering edit mode
6.3 years ago
GenoMax 123k

See this thread. It should still be applicable.

ADD COMMENT

Login before adding your answer.

Traffic: 1257 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6