I am trying to get the location of miRNAs on the human genome GRch37 from UCSC.
I tried to use bioconductor to do this. According to documentation, if I understand well you do:
But I get an empty TranscriptDB...:
GRanges with 0 ranges and 1 metadata column:
seqnames ranges strand | mirna_id
<Rle> <IRanges> <Rle> | <character>
chr1 chr2 ... chrUn_gl000249
249250621 243199373 ... 38502
I investigated and found that:
-for TxDb.Hsapiens.UCSC.hg19.knownGene, I have: "miRBase build ID: GRCh37" -for mirbase.db: supportedMiRBaseBuildValues() gives me:"Homo sapiens GRCh37.p5"
I fear that there is an incompatibility here and I do not know what to do to make it work. Would you have any idea please?
If not, would you know where I could getthe locations for the microRNA on GRch37 please??