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RabadanLab / Pegasus

Annotation and Prediction of Oncogenic Gene Fusions in RNAseq
MIT License
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Empty annotation columns #2

Open patterja opened 7 years ago

patterja commented 7 years ago

The 16 columns to the right of Kinase_info, including Transcript_ID1 to Lost_Domain2 are empty in the pegasus.output.txt when running the examples in sample_pipeline_input directory. These columns have value "NULL" in final_results_forXLS.txt file. Your example file includes BCR-ABL fusions and I'm pretty sure there should be some output for these annotated columns for at least this fusion gene. There are no error messages when executing, but based on the content and time of access of the log files, the Merge_format.log and Merge_format.job are both empty. Is this package still being maintained?

casi1212 commented 6 years ago

Hello patterja, I am getting the exact same issue with Pegasus. Did you ever end up resolving the problem? Thanks-

patterja commented 6 years ago

I did not resolve this issue. I ended up using some other fusion annotation open source tools that are actively updated and maintained, which is probably better in the long run anyway, with some additional scripting to query specific databases I wanted include in my annotation.

casi1212 commented 6 years ago

What program did you end up using? Thanks so much -

                                                                                     ~Monica

From: Janice Patterson notifications@github.com Sent: Monday, July 9, 2018 3:31:10 PM To: RabadanLab/Pegasus Cc: Wei, Monica; Comment Subject: Re: [RabadanLab/Pegasus] Empty annotation columns (#2)

I did not resolve this issue. I ended up using some other fusion annotation open source tools that are actively updated and maintained, which is probably better in the long run anyway, with some additional scripting to query specific databases I wanted include in my annotation.

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