[Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

Rainer Johannes Johannes.Rainer at eurac.edu
Fri Jan 8 11:37:08 CET 2016

dear all,

I just run into a problem with a TwoBitFile I fetched from AnnotationHub. I was fetching a TwoBitFile with the genomic DNA sequence, as provided by Ensembl:

> library(AnnotationHub)
> ah <- AnnotationHub()
> tbf <- ah[["AH50068”]]

> head(seqnames(seqinfo(tbf)))
[1] "1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF"  
[2] "10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF"
[3] "11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF"
[4] "12 dna:chromosome chromosome:GRCh38:12:1:133275309:1 REF"
[5] "13 dna:chromosome chromosome:GRCh38:13:1:114364328:1 REF"
[6] "14 dna:chromosome chromosome:GRCh38:14:1:107043718:1 REF"

Would be nice, if the seqnames would be really just the chromsome names and not the whole string from the FA file header. Is there a way I could fix the file myself or is this something that should be fixed in the rtracklayer or AnnotationHub package when the TwoBitFile is created?

thanks, jo 

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