Hi Malcolm,
In general I have found ensembl to be really great and I expect that
their gtf files are probably fine. Usually the exon rank is the 1st
thing you will see left out when a gtf file is cutting corners, and you
are correct that they seem to be including that. I ran the one for Homo
Hi Tengfei,
Yes that looks like an oversight. Thanks for reporting that! I will
extend makeTxDbPackage so that it's more accommodating of these newer
transcriptDbs. If you want to help me out, you could call saveDb() on
your gmax189 object and send me the .sqlite file that you save it to.
.Hi Tengfei,
.
.Yes that looks like an oversight. Thanks for reporting that! I will
.extend makeTxDbPackage so that it's more accommodating of these newer
.transcriptDbs. If you want to help me out, you could call saveDb() on
.your gmax189 object and send me the .sqlite file that you save
Dear all,
I am trying to build a txdb object from gff3 for soybean data and try to
make it a package. Code used like this
gmax189 - makeTranscriptDbFromGFF(~/Gmax_189_gene_exons.gff3,
format = gff3, species = Glycine max,
