Using a non-zipped file

[bluessherpa]

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

Thanks.
Novis John

[wdecoster]

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]

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 GitHub<#16 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AUVF9AuVnPpIUE1XrmPt5-YfGYWb9IGhks5tRyxTgaJpZM4R5tk6>.

[wdecoster]

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

[bluessherpa]

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

[wdecoster]

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