Question

Tophat: Compressed Fastq File (Gz)

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12.7 years ago

Nicolas Rosewick 11k

Hi,

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

Thanks,

N.

tophat • 11k views

ADD COMMENT • link updated 9.4 years ago by Biostar 20 • written 12.7 years ago by Nicolas Rosewick 11k

score 3 · Answer 1 · 2012-03-16

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12.7 years ago

Sean Davis 27k

Yes. It will uncompress based on the filename extension.

ADD COMMENT • link 12.7 years ago by Sean Davis 27k

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Thanks a lot !

ADD REPLY • link 12.7 years ago by Nicolas Rosewick 11k

score 0 · Answer 2 · 2012-03-18

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12.7 years ago

Science_Robot ★ 1.1k

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 ...

ADD COMMENT • link 12.7 years ago by Science_Robot ★ 1.1k

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

ADD REPLY • link 12.7 years ago by Sean Davis 27k

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

ADD REPLY • link 12.7 years ago by Science_Robot ★ 1.1k

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

ADD REPLY • link 11.7 years ago by Ryan Thompson ★ 3.6k

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For a general solution, you can often do:

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

ADD REPLY • link 11.7 years ago by Sean Davis 27k