Rename Tophat 'accepted_hits.bam' file

[pachapep]

Dear all,

I have mapped some reads using Tophat, which gives me a accepted_hits.bam file that I am trying rename to new.bam (and then index).
Is there an simple way to do this directly using a TopHat parameter? I mean, give a name to use as the output file? Thanks

p.

[Bukowski]

Short answer, no.

Slightly longer answer, is that you can specify the output directory with a name parameter: -o which is what we do in our pipelines to separate out the samples. But that is it as far as your renaming options go. Unless there is an undocumented output file function.

[pachapep]

So I just add the name after the -o and it should do the trick? Or is it just the name of the directory? For now, I am filtering by dir names, but I still get an accepted_hits.bam in each dir.. Thanks

[GenoMax]

-o creates a top level directory with the name you provide. Set of files created inside are still all named exactly the same (including accepted_hits.bam) for each sample. There is nothing preventing you from renaming the file to something else for further analysis/indexing afterwards. You may be able to create a soft link and then use that name to index.

Edit: Soft linked names pointing to accepted_hits.bam file work for sorting/indexing with samtools.