Tophat2 specify output file

[vishalthapar]

Hi All,

This is a basic question wrt Tophat2 output. I want to name the output of tophat in the ./tophat/ to another name apart from "accepted_hits.bam". Is that possible? If so, how?

The reason is that I am trying to split the fastq file into multiple parts and run this in parallel. In the end, I shall combine all the output files into 1 bam files. As of now, Tophat will overwrite "accepted_hits.bam" and I will only get the last output instead of all the individual files.

Thank you for your help.

Best,

Vishal

[Richard Barker]

you could try the iplant system

If you use the TopHat GUI based application within the iplant discovery environment (http://www.iplantcollaborative.org/d...ry-environment) then it automatically produces a BAM file with the same name as the original FASTA file you put in along with the normal outputs in a separate folder.

[vishalthapar]

Thank you Richard. I am actually using it on the command line. I am guessing if it can be done using the GUI then it can be done with the command line as well. Thanks,

Vishal