Mapping to a single Chromosome Tophat

Question

[benjyrolls]

I have a data set which relates to all the chromosomes which has been mapped to a whole genome using Tophat so this eventually produces mapped reads, but for all the chromosomes,

from these mapped reads output from tophat how do I obtain, the reads mapped to only one chromosome say chromomosome 1 only?

Answer 1

[Benn]

This has been asked and answered before, use samtools.

See e.g.,

How to generate a .sam/.bam file of a particular chromosome or even a particular region?

Answer 2

[Devon Ryan]

Since you used the Galaxy tag, I'll assume that you're doing this in Galaxy. In that case, you can use the "Filter SAM or BAM, output SAM or BAM" tool.