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Tophat: Compressed Fastq File (Gz)

Hi,

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

Thanks,

N.

tophat
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updated by Biostar Biostar • written by Nicolas Rosewick Nicolas Rosewick

2 answers

Yes. It will uncompress based on the filename extension.

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written by Sean Davis Sean Davis

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 ...
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written by Science_Robot Science_Robot

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

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written by Sean Davis Sean Davis

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

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written by Science_Robot Science_Robot

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

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written by Ryan Thompson Ryan Thompson

For a general solution, you can often do:

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

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written by Sean Davis Sean Davis

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