Tophat Multiple inputs and out puts

[repinementer]

Hi

I have 5 fastq files. Is it possible to run tophat on every one at the same time and get 5 outputs with a single command ? [ SAM files ] ?

In general Tophat accepts multiple files and gives a single output but in my case i need multiple outputs (for 1 input 1 output)

[dariober]

Hi

I have 5 fastq files. Is it possible to run tophat on every one at the same time and get 5 outputs with a single command ? [ SAM files ] ?

In general Tophat accepts multiple files and gives a single output but in my case i need multiple outputs (for 1 input 1 output)

I don't think tophat can output one file per input.

If your reads come from an Illumina sequencer and if they have been run on different lanes (or on different instruments), then you could parse the tophat output on the bases that read names begin with 'instrument ID':'lane number'.

E.g.:
EBRI093151_0001:7:1:479:1994#TCCACC
Instrument name= EBRI093151_0001
Lane= 7

Alternatively you could match the SAM output against the 5 inputs although I not sure read names are guaranteed to be unique across runs.

Dario

[fkrueger]

There have been some helpful comments in this thread:

http://seqanswers.com/forums/showthread.php?t=7259&highlight=tophat