dbprep tool

[CentreFrançoisBaclesse - Bioinfo]

Hello,

I try to create transcript database, but I got this error message :

$ python dbprep.py -i transcripts.txt -e 75 -o outputGRCh37

-----------------------------------------------------------------

CAVA v1.1.1 dbprep (database preparation script) is now running.

Started:  2015-09-16 15:42:26.563913 

Ensembl version:  75

Reference genome: GRCh37

35 transcript IDs read from transcripts.txt.

Downloading Ensembl database... OK

Extracting transcript data... Traceback (most recent call last):

  File "dbprep.py", line 405, in <module>

    createFile(options)

  File "dbprep.py", line 28, in createFile

    n=generateTranscriptDB(options)

  File "dbprep.py", line 146, in generateTranscriptDB

    finalizeAndOutput(outfile,transcript)

UnboundLocalError: local variable 'transcript' referenced before assignment

Best, 

[Márton Münz]

Hi,

The dbprep command you used is correct and is working well on our computer. Could you please send me the transcripts.txt file so that I can try with that as well? I'm trying to reproduce the error you got.

Thanks!

Best, 

Marton

[CentreFrançoisBaclesse - Bioinfo]

Hi, 

I have found why the command not working. 

I filled transcript file with HGNC RefSeq ID. 

I would like to know if it's possible to annotate variants with RefSeq Id. 

Best, 

[Márton Münz]

Hi,

No, CAVA currently only supports Ensembl transcripts.

Best,

Marton

[Elise Ruark]

To annotate variants with RefSeq IDs, you would need to find the corresponding Ensembl ENST ID using something like Ensembl's BioMart tool. You can then supply those to CAVA, and it will return the HGNC symbol (e.g. BRCA1) in the annotation.

The caveat here, of course, is that RefSeq transcript sequence is not necessarily the same as Ensembl transcript sequence (which is reference genome sequence), for instance when the RefSeq transcript contains a major allele which is not the reference genome allele.

Best,

Elise

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