Jbrowse feedback from petra

[cybersiddhu]

• Why are all tracks dark yellow when way zoomed out? Not tragic, just confused me the first time (you know how color-cued I am)
  • It turns into a histogram at a higher zoom level.
• I tried the sequence search track (File/Add sequence search track). However, I don’t quite understand, it doesn’t go to the searched sequence stretch (I searched for a stretch of sadA protein and cDNA sequence).
  • How do we figure out if it had hit a particular stretch of sequence in the genome ?

• Search: I First tried adding a gene name on the upper left, in the track search field although it was obvious this shouldn’t work. Then I simply tried searching for gene names in the box with the coordinates and this works! However, a non-clicker might not find this. Is it possible to configure that this search box is on the left of the navigation tools instead on the right? This might help somewhat.

  • Either the search box in left of the panel
  • Or make it visible by having a different background color.

  For this we need to consult jbrowse mailing list.

• I saw the save track data for each individual track, but not the possibility to just download the Fasta sequence from the gene model?
  • Right click on the track and from the dropdown select details. The details panel will give an option to download fasta.
• The Reference Sequence track: I still have to play with that a bit more, but I guess only the Dd genome sequence is visible now and it will only be usable when we have another strain?

[cybersiddhu]

• Decorated fasta files
  • We might have to write a plugin for it
  • Also ask jbrowse mailing list for feedback