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LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq
http://starchimp.readthedocs.io/en/latest/
MIT License
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Empty output files #28

Open QuentinLetourneur opened 5 years ago

QuentinLetourneur commented 5 years ago

Hello,

I run starchip on Ubuntu 16.04 I've started to use Starchip-fusion. I ran it with default parameters. There is a problem with output files. After a successful run, out.summary and out.summary.annotated only contain the header. But out.summary.temp and out.summary.temp.annotated (I kept them by commenting the cleanup part) are complete.

Best regards, Quentin

kippakers commented 5 years ago

Hi Quentin,

The temp files keep fusions that are excluded for various reasons (e.g. they appear to be circRNA, it looks like a long splice within a gene, etc). Your stdout should have given some information about this. So if your final output files are empty and you haven't gotten any error messages, I believe that means STARChip didn't find any fusions that it likes.

Cheers, Kipp

QuentinLetourneur commented 5 years ago

I now understand what was going on. I gave an empty gtf file and I didn't get any prompt after the start of the annotation. I assume it's like skipping this step. Maybe you can add a prompt or error to notify the user if the gtf file is empty.

Best, Quentin

kippakers commented 5 years ago

Thanks for the info, I wasn't aware of this behavior. I'll try to replicate and add a check for an empty gtf file.
Cheers, Kipp