My use case is as follows:
I have aligned RNA-Seq data using tophat2 and a GTF file I got from Ensembl. Now I would like to produce alignment stats (number of reads mapping to exons, introns, intergenic regions) and, it seems, the CollectRnaSeqMetrics script from the Piccard toolset would be the most straight-forward to use. However, it requires annotation in RefFlat format (why on Earth there have to be so many different annotation formats??). So now I would like to convert GTF to RefFlat format. There is, apparently, a tool called gtfToGenePred which is supposed to do this but I could not find a manual or documentation for it. Can anyone provide info on converting GTF files to RefFlat format? Alternatively, can you suggest a way I can get the alignment stats using a GTF annotation file?
I have aligned RNA-Seq data using tophat2 and a GTF file I got from Ensembl. Now I would like to produce alignment stats (number of reads mapping to exons, introns, intergenic regions) and, it seems, the CollectRnaSeqMetrics script from the Piccard toolset would be the most straight-forward to use. However, it requires annotation in RefFlat format (why on Earth there have to be so many different annotation formats??). So now I would like to convert GTF to RefFlat format. There is, apparently, a tool called gtfToGenePred which is supposed to do this but I could not find a manual or documentation for it. Can anyone provide info on converting GTF files to RefFlat format? Alternatively, can you suggest a way I can get the alignment stats using a GTF annotation file?
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