Tophat: Compressed Fastq File (Gz)

Question

[Nicolas Rosewick]

Hi,

Is it possible to use Tophat with .gz fastq file ?

Thanks,

N.

Answer 1

[Sean Davis]

Yes. It will uncompress based on the filename extension.

[Nicolas Rosewick]

Thanks a lot !

Answer 2

[Science_Robot]

If you ever have a program that doesn't accept gzipped input or you're not sure whether or not it accepts gzipped input, you can make it using UNIX pipes:

gzcat the_file.gz | program -in /dev/stdin ...

[Sean Davis]

That works if there is only one input. If there are multiple, one must resort to fifos.

[Science_Robot]

What about gzcat the_files*.gz | program -in /dev/stdin ???

[Ryan Thompson]

That is multiple input files but still one input. Tophat takes two inputs for paired-end sequencing data.

[Sean Davis]

For a general solution, you can often do:

program -in1 <( gzcat inputfile1.gz ) -in2 <( gzcat inputfile2.gz )