How I can extract the sequences of short reads mapped to a particular gene in genome in RNA-Seq
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?
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Biostar
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ebrahimiet •
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ebrahimiet •
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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.