Closed mrshu closed 6 years ago
@ViRPo anything I can help with here (so that we can close this)?
@mrshu it should be complete now :)
@ViRPo very cool, thanks!
I have found a small problem with this track: it seems that the browser has built-in different behavior for tracks named tRNAs. If you click on a particular tRNA gene (e.g. http://genomika.compbio.fmph.uniba.sk/cgi-bin/hgTracks?db=malGlo1&position=NW_001849856.1:157031-157115 ), you will get an automatically generated info page about this gene which uses columns of our bed file incorrectly, leading to nonsense. For example, anticodon should be GCC here, not 157030.
One way would be to parse tRNAscan-SE output differently, producing a BED file more similar to tRNA tracks in the UCSC genome browser http://genome-euro.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=genes&hgta_track=tRNAs&hgta_table=tRNAs&hgta_doSchema=describe+table+schema
However, I would suggest a simpler approach: rename the tRNAs track differently, e.g. only tRNA (drop tRNAs table from the database, load again to tRNA table, change trackDb.ra, make alpha,...)
I did as suggested
However, I didn't check what the parsed output looked like before these changes, so I don't know whether the output changed at all, but it seems OK to me
Looks good