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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Small RNA pipeline - issue with tdrmapper #1352

Closed AurelieMLB closed 8 years ago

AurelieMLB commented 8 years ago

Hello,

My understanding was that there should be a mapping to known tRNA using tdrmapper (http://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html#smallrna-seq) and that there should be a folder in final or inside sample folders. After I tried to run the pipeline, I cannot find this folder at all. I did search for tdrmapper in the nohup.out in the work folder it seems that there is no mention of it. So it is like the pipeline was not trying to launch it at all. Yet there is a TdrMappingScripts.pl in the bcbio app folder that we have... In the work folder of my run, I do have a trna folder which seems to give the mapping for each samples. I am not sure it is the expected output of tdrmapper compared to this.

Many thanks for any help

lpantano commented 8 years ago

Hi, will close this since the problem is the same than #1353. Thanks for the detailed information.