search

timbitz / Aligater

Software suite for detection/analysis of chimeric RNAs from LIGR-seq data
MIT License
2 stars 1 forks source link

hgSQLBasics missing? #1

Closed riasc closed 7 years ago

riasc commented 8 years ago

Hello, as I'm working on something similar, so aligater caught my attention. I was trying to reproduce the analysis with aligater, but somehow couldn't get it to work with the default parameters. The hgSQLBasics module seems to be missing at it is in the intRagenic repository. Or what am I missing? Just piping the results from aligater align should be sufficient? Also I can't get any usage information on the specific aligater steps with -h, e.g., aligater detect -h but I guess thats still to come.

Cheers. Richard

timbitz commented 8 years ago

Hey Richard, Sorry to take so long with this. I'm not really developing this actively at the moment and so I apologize for the lack of documentation and that missing dependency!...

As a quick fix, I added that library, even though its mostly not used. Additionally as of #2 I have fixed the broken link to the database, and added a bit of documentation which should be sufficient to reproduce the analysis.

Please let me know if there is anything missing or unclear..

Cheers, -t