Hello, I'll try to address your questions in line with your email - so please see below ....
Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jie Huang (NIH/NHLBI) [F]" <[email protected]> wrote: > From: "Jie Huang (NIH/NHLBI) [F]" <[email protected]> > To: [email protected], "Jennifer Jackson" <[email protected]> > Sent: Friday, November 13, 2009 1:46:59 PM GMT -08:00 US/Canada Pacific > Subject: a final round of questions on UCSC GENOME GRAPHS > > Hi, Jennifer: > > Sorry to keep asking you some more questions. This should be pretty > much my final list of questions as I am trying to figure things out. > No problem, we are glad that you find the tool useful > please see the attached screenshot of a Genome Graphs session that i > created. > > 1. how to make the track name show on the graph? Right now, the track > name only shows on the top of the drop-down menu. When I have 10 > tracks, it would be hard for me to remember which track is what? > Ideally, the track name should show up to the left of each track > graph. This is very good idea. Tracks are labeled in the Assembly browser in a similar way (not to the left, but above). I will pass this on to the scientific development team for consideration. > > 2. how to change track name? i found that all track names was > automatically named something like "track name 1" with an appending > "1". But I really want to change that since users will get confused, > thinking there might be a "2" or something. The track is named when added to the graphing tool (short label). Why they are numbered I am not exactly sure - I will ask and get back to you. > > 3. after i open a saved session and make some change, how do save the > change to this session like how we edit and save a Word document? do i > have to delete the old session and save it as the same name? > While inside of the original Session, to save the new configuration just save the same way as for the first round, but give it a new name to preserve both versions. A Session can have many saved configurations based on the same underlying data as long as they are named differently. > 4. you might be aware of the "Genetic Associations: (NHGRI Catalog)" > track at Hapmap Browser. However, it is static with just blank dots. > So, I tried to put the GWAS Catalog into UCSC browser so that users > can explore interactively. I generated the text file at > http://people.bu.edu/jiehuang/Catalog.txt and the according UCSC > browser link is > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&hgt.customText=http://people.bu.edu/jiehuang/Catalog.txt > Can you see if your group might be interested in having something like > this and make it much better?! Another good idea that I will pass on. > > 5. just to confirm, any named session will be saved for 1 year after > last use, and any unnamed session will be only saved for 48 hours, > right? I would not want my named session suddenly disappear after a > couple of days of inactivity. Data (custom track or native) and the browser settings are saved on our server for an extended period of time when it is in a Session (as opposed to just a regular Custom Track). It is a bit flexible - we try to keep for at least a year. However, we do recommend that you download a saved copy of any session that you would miss if it was lost. Unexpected data loss can occur (and has occurred) in the past due to server failures. This is rare, but possible, so it is worth it to be prepared. > > I realize that you must have a lot to do, and I would really > appreciate if you could give some quick feedback on these questions. > > Best regards & have a wonderful weekend!!! You, too! Jennifer > > Jie _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
