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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
