Maybe it's just me, but the only GTF reference file that seems to work in TopHat (when using the -G option that is) is refFlat (RefSeq) downloaded from the UCSC Table Browser. Any other GTF file I download from there (e.g., ensGene) or ENSEMBL (following the recommendation in the TopHat website) just doesn't work (i.e., I get the "TopHat did not find any junctions in GTF file" warning) .
I know the problem has popped up in this forum multiple times. Therefore, I would like to get as much feedback as possible as to which GTF files people are using for their RNAseq analysis. And whether anybody has managed to get the ENSEMBL gene annotation to work.
Thank you in advance for your help and consideration.
I know the problem has popped up in this forum multiple times. Therefore, I would like to get as much feedback as possible as to which GTF files people are using for their RNAseq analysis. And whether anybody has managed to get the ENSEMBL gene annotation to work.
Thank you in advance for your help and consideration.
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