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dlampart / Pascal

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Gencode annotation #5

Open kvetab opened 4 years ago

kvetab commented 4 years ago

Hello, I am using the Pascal package, which contains an annotation file with UCSC known genes. However, I would like to use it with ENSG identifiers. In the settings.txt file included in the package I found this: 

#genomeAnnotation = gencode
# Gencode annotation (use for ENSEMBL gene IDs)
genecodeAnnotationFile = resources/annotation/gencode/gencode.v18.annotation.genes.gtf

but the actual file is nowhere to be found (the directory annotation only contains bed, hla, and ucsc). I also considered using a file I'd create myself based on data downloaded from Ensembl. Could you please provide either the file mentioned above or some guidelines for how to use Pascal with a custom annotation file? Thanks in advance.

pratinhos commented 3 years ago

Apologies for ressurecting this issue, but I am also having trouble with this.

I have managed to get the analysis running with a gencode file that I have prepared after some trial and error: basically I downloaded a gencode .gtf file and removed all the lines/entries except the ones that referred to genes in the third column. However, for some reason that I am yet understand, I am getting 0 SNPs for every single gene in the analysis, and thus, an empty genescore file. Any idea?