How I can extract the sequences of short reads mapped to a particular gene in genome in RNA-Seq

Question

[ebrahimiet]

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?

[vakul.mohanty]

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.

Answer 1

[GenoMax]

See this thread. It should still be applicable.