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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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--filter-out and --filter-out2 #437

Closed nktkee closed 4 years ago

nktkee commented 4 years ago

Hi,

I'm wondering how to get the --filter-out option working, where reads that don't match a UMI are sorted out into a separate file?

cheers, nk

TomSmithCGAT commented 4 years ago

You should just need to add the argument --filtered-out=FILENAME, replacing FILENAME with the path to where you wish to write out the filtered reads. If you have a paired input, you will need --filtered-out2=FILENAME2 also.

TomSmithCGAT commented 4 years ago

@nktkee - Did you get this working OK?

Evelyn2579 commented 4 years ago

I have the same problem with nk. I used --filtered-out=filename, but it reported an error: extract: error: no such option: --filtered-out. also wondering how to get the argument --filtered-out=filename work

TomSmithCGAT commented 4 years ago

@Evelyn2579 - That's very strange. What version of are you using? (umi_tools --version)

vincenthahaut commented 4 years ago

I face the same issue. The option seems to have vanished (including from the -h help).

UMI-tools version: 1.0.1

EDIT: It seems that these are new add-ons from 1.1.0.

TomSmithCGAT commented 4 years ago

@Radek91 - You're right. The PR with this option (#330) wasn't merged until 13 AUG 2020, and no release was made until 1.1.0 on 03 NOV 2020, which explains why this option wasn't available to @Evelyn2579 & @nktkee, who I assume installation via pip or conda. I'd overlooked the difference between the master branch and the latest release.

Since the option is now available on the latest release, I'll close this issue now. If anyone else is having the same problem, please make sure you are using version >= 1.1.0.