CTAT_splicing no cancer introns identified

[Aaron De Cock]

Hi, 

We've been running the CTAT-splicing tool on a couple of RNAfusion runs that were analysed with nf-core/rnafusion v3.0.1. 

recently we had to rebuild the references for this rnafusion pipeline and also those for the ctat-splicing tool. 

after installing the CTAT-splicing data resource supplement everything seemed to work again, the tool finished without errors, however, no cancer introns were detected (which is strange on the data we have). So we tried running the ctat-splicing tool again on old data which was already analysed with the ctat-splicing tool. But also no cancer introns were detected. 

I suspect there might be something wrong with the references or the cancer_splicing_lib. 

Can you confirm the cancer_splicing_lib folder only has a cancer_splicing.idx file after integrating the CTAT-splicing data resource supplement? 

Do you know how we can best troubleshoot this issue? GRCh38 is used for both the rnafusion pipeline and the ctat-splicing tool.. 

Kind regards, 

Aaron De Cock 

[Brian Haas]

Hi Aaron,

It should just require that the cancer_splicing_lib/cancer_splicing.idx

be incorporated into your ctat genome lib directory.

You can try rebuilding that by going through the ctat splicing prep steps again - just make sure you're using the ctat splicing GRCh38 version from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/

Can you try running the test that's in the CTAT_SPLICING software repo?

eg.

       cd      ~/GITHUB/CTAT_SPLICING/testing 

       make

This should give a report with found splicing aberrations if it's working as expected.

best,

Brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas