liulab / MAGeCK-VISPR / issues / #9 - Counts returning all zeros — Bitbucket

Issue #9 new

bibaswanghoshal created an issue 2016-10-19

Hi,

I am running mageck-vispr version 0.5.3. After running the test dataset, the pipeline returned all zero counts. I can't figure out what is going wrong. I am attaching the log file as well.

Thanks,

Bibaswan

Screen Shot 2016-10-19 at 9.31.20 AM.png

Comments (6)

bibaswanghoshal reporter
- edited description
- 2016-10-19T13:34:15+00:00
bibaswanghoshal reporter
- attached myexperiment1.log
- 2016-10-19T13:34:40+00:00
Johannes Köster
- assigned issue to
  
  Wei Li
- 2016-10-19T13:35:20+00:00
Johannes Köster
Assigning to Wei, because this is a Mageck related issue. My guess is that there is a problem with your library file.
- 2016-10-19T13:36:13+00:00
bibaswanghoshal reporter
The library file I used was the one provided in the example test2 dataset "yusa_library.csv".
- 2016-10-19T13:39:14+00:00
Wei Li
Is this the test dataset? If yes, you should trim 5' reads to 23 nt, not 5nt. That's why you get 0 read counts.
- 2016-10-19T17:46:04+00:00
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Assignee: Wei Li

Type: bug

Priority: major

Status: new

Votes: 0

Watchers: 1

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