Question: Genome Browser suggestions
2
gravatar for Macspider
15 months ago by
Macspider2.6k
Vienna - BOKU
Macspider2.6k wrote:

Hi all,

I am in search of a Genome Browser that could suit my needs. I already used many times GBrowse, IGV and Jbrowse. GBrowse is too tedious to work with given the way you have to add tracks and given that is very slow when the database becomes big. JBrowse is awesome but doesn't feature an SVG export as GBrowse instead does. IGV is nice but the image export sucks in quality. What I'm searching for now is a GB that:

  1. Is faster than GBrowse
  2. Can export SVG images
  3. Has a nice layout that suits publication-level images (i need many of them)
  4. EDIT: supports reference genome upload from files

Do you guys have any suggestion? Please don't suggest anything that doesn't fulfill all of these 3 criteria: I probably have already tried it out and discarded it :D

Thanks!

ADD COMMENTlink modified 15 months ago by jrj.healey9.2k • written 15 months ago by Macspider2.6k
1

See: A: Portable genome browser

ADD REPLYlink written 15 months ago by genomax59k

May I ask what problems you had with IGVs quality? Did you export as SVG?

ADD REPLYlink written 15 months ago by ATpoint11k

The version I have of it doesn't support it. In case modern versions do, then I would upgrade it.

ADD REPLYlink written 15 months ago by Macspider2.6k
1

2.3.79 does support png, svg and jpeg.

ADD REPLYlink written 15 months ago by ATpoint11k

What version are you using? I thought IGV always had SVG export. IGV is currently v. 2.3.97.

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax59k

Fixed. I am using IGV with sVG export now. The thing was: we had IGV on a node which was usually logged in to without -X, and could for some reason render png but not svg (don't ask me why, perhaps some graphic libraries not loaded). Now it exports nice SVGs!

ADD REPLYlink written 15 months ago by Macspider2.6k
3
gravatar for dariober
15 months ago by
dariober9.8k
Glasgow - UK
dariober9.8k wrote:

Full disclosure: I'm the author of it. I wonder if ASCIIGenome is any use to you?

It has a different approach from the other browsers as it is controlled via the command line, either interactively or automated (with some optimism I like to think of it as the vim of genome browsers). It displays genomic data directly to the terminal screen, as such it is easy to automate and since you say you have lots of images to print it may help.

It can save pictures in text or pdf format so figure quality is not an issue, but of course, it deliberately doesn't have the fancy layout of IGV and similar. The reference genome can be loaded from fasta file.

Here's an example in non-interactive mode:

ASCIIGenome -ni -x 'save test.pdf' ds051.actb.bam

The pdf figure looks like

ADD COMMENTlink modified 15 months ago • written 15 months ago by dariober9.8k

I doesn't go in the direction of what I need but it's fancy and super cool, I think I will try it out for my personal purposes! :)

ADD REPLYlink written 15 months ago by Macspider2.6k

Thanks for your comment - Feel free to drop an issue on github or a post here on biostars if you have any questions.

ADD REPLYlink written 15 months ago by dariober9.8k

Does ASCIIGenome support navigation using the arrow keys?

ADD REPLYlink written 15 months ago by genomax59k

Hi- There are a few options to navigate but they don't use the arrow keys (!). The UP and DOWN keys scroll commands like in most terminal shells. To move left and right one can use keys f and b (forward/backwards) or +10k and -10k to move 10kb forward or backwards. More on navigation here.

Unfortunately, I must admit the navigation is not as smooth as in samtools tview since between one execution of a movement and the next there is a bit of delay (sort of similar to IGV I guess).

ADD REPLYlink modified 15 months ago • written 15 months ago by dariober9.8k

Would be useful if you can support <- and -> arrow keys along with with some additional combination (ctrl + arrow etc to allow longer jumps 100kb etc)? I tend to use the arrow keys for navigation on the command line and they feel like a natural extension of what is happening on the display.

Is there a specific reason for requiring a return after pressing f/b keys? I noticed that subsequent simple returns are used to repeat the last f/b directive. Perhaps that is the reason?

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax59k

Thanks for comments! Of course, I see what you mean about arrow keys being more intuitive. The reason for "return" after a command is to send the input string to ASCIIGenome which then it interprets it as appropriate, just like you need ls followed by <ENTER> at the Bash terminal. A subsequent ENTER will repeat the previous command, whatever that was. It may be possible to map the left and right keys to some behavior like f/b, but I'm not sure...

About long jumps, it's a bit tricky to define a "good" behavior since, for example, 100kb may be a big jump in some cases but a small jump in others. For this, f/b move by default 1/10 of the current genomic window, which roughly is a small jump. However, you can pass a number to f/b to make the window move by a proportion of the genomic window, e.g. f 0.5 moves forward 1/2 of the current window (and this is the same as the ff/bb commands). Then of course, for jumps of a defined size you can use +/-INT as I mentioned above.

ADD REPLYlink written 15 months ago by dariober9.8k

It may be possible to map the left and right keys to some behavior like f/b

That would be great. It would allow one to scroll left/right seamlessly without having to hit the keyboard for f/b. Is the screen jump/move interval configurable?

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax59k
2
gravatar for Charles Plessy
15 months ago by
Charles Plessy2.6k
Japan
Charles Plessy2.6k wrote:

How about ZENBU ?

Here is an example illustration that I made starting from ZENBU's SVG export.

ADD COMMENTlink written 15 months ago by Charles Plessy2.6k

Thank you, this looks nice. Can I load my reference genome? Because I don't work with a canonical organism.

ADD REPLYlink written 15 months ago by Macspider2.6k

It's work in progress. At the moment you would need to contact the browser admin.

ADD REPLYlink written 15 months ago by Charles Plessy2.6k
1
gravatar for simon.vanheeringen
15 months ago by
simon.vanheeringen170 wrote:

Why not use the UCSC Genome Browser? You can add tracks using track hubs and support non-standard genomes using assembly hubs, see here: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html. The advantage of track hubs is that you only have to create them once, and then you can use always use your tracks, configured as you like them. No SVG export, but there is PDF export which is easily converted.

ADD COMMENTlink written 15 months ago by simon.vanheeringen170

UCSC Genome Browser is waaaaaay too slow for my needs (I tried).

ADD REPLYlink written 15 months ago by Macspider2.6k
1

Was there anything in particular that was too slow? I can create a bug report for it if there was something specific.

Thanks, ChrisL from the UCSC Genome Browser

ADD REPLYlink written 15 months ago by genecats.ucsc560

I don't think it's a problem of UCSC Genome Browser itself, but more of its interaction with our system. We basically have to find one that works fine with our set-up (I am not the sysadmin so I can't go further in details here, I would go out of my league).

ADD REPLYlink written 15 months ago by Macspider2.6k
1
gravatar for Alex Reynolds
15 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

UCSC Genome Browser + soda.py for automated PDF figure generation.

ADD COMMENTlink written 15 months ago by Alex Reynolds26k
0
gravatar for jrj.healey
15 months ago by
jrj.healey9.2k
United Kingdom
jrj.healey9.2k wrote:

I almost exclusively use ARTEMIS

ADD COMMENTlink written 15 months ago by jrj.healey9.2k
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