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wdecoster / nanofilt

Filtering and trimming of long read sequencing data
GNU General Public License v3.0
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Using a non-zipped file #16

Closed bluessherpa closed 6 years ago

bluessherpa commented 6 years ago

Is there a way to get NanoFilt to work without using a zipped file?

Thanks. Novis John

wdecoster commented 6 years ago

Hi,

Certainly. Instead of using gunzip/zcat you can simply use cat to stream the file. Is that what you are looking for?

Cheers, Wouter

bluessherpa commented 6 years ago

I guess it is how it would be written in the command line

John P. Fellers, Ph.D. Research Molecular Biologist

USDA-ARS-HWWGRU Dept. of Plant Pathology 4008 Throckmorton Hall Manhattan, KS 66506 785.532.2367 fax 785.532.6167

On Feb 5, 2018, at 10:29 AM, Wouter De Coster notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

Certainly. Instead of using gunzip/zcat you can simply use cat to stream the file. Is that what you are looking for?

Cheers, Wouter

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/wdecoster/nanofilt/issues/16#issuecomment-363138465, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AUVF9AuVnPpIUE1XrmPt5-YfGYWb9IGhks5tRyxTgaJpZM4R5tk6.

wdecoster commented 6 years ago

cat myfile.fastq | NanoFilt -q 10 > myfilteredfile.fastq

bluessherpa commented 6 years ago

Thank you very much!!!!! It worked great!!!

wdecoster commented 6 years ago

Please let me know if that doesn't work, or if you have other issues, suggestions or feature requests.