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elsiklab / sashimiplot

A JBrowse plugin for creating sashimi or junction style plots from RNA-seq data
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Is it OK with large bam files? #1

Closed billzt closed 8 years ago

billzt commented 8 years ago

The plugin requires bam file input. Is it OK with large bam files? For many RNA-seq mappings to a large (several GB) reference genome, the result bam file is usually several GB large

cmdcolin commented 8 years ago

Should be fine with pretty large BAM files. It is a little intensive, but not any more intensive than the default Alignments2 tracks, and maybe even less so because it doesn't have to draw as many things to the screen.

I was also thinking of allowing the input to be read from junctions.bed files for example, but I haven't gotten around to that yet.

cmdcolin commented 8 years ago

Also there might be an issue when viewing a very large area. It's possible that adding a "scale" limit to tell the user to zoom in to view more would be useful

billzt commented 8 years ago

Thanks. I'll try it

cmdcolin commented 8 years ago

No worries! Here is a quick guide for installing the plugins that could help :) http://gmod.org/wiki/JBrowse_FAQ#How_do_I_install_a_plugin

billzt commented 8 years ago

Well, I still hope allowing the input to be read from junctions.bed. File junctions.bed is much smaller than bam file. My disk space is poor...

cmdcolin commented 8 years ago

Agree!

cmdcolin commented 8 years ago

Should be fixed to allow junctions.bed now

Simply load the file with flatfile-to-json.pl, and then change the track "type" in trackList.json to SashimiPlot/View/Track/Sashimi

I added a sample configuration to README.md for this :)

cmdcolin commented 8 years ago

Note that interestingly, the "useXS" option still works with junctions.bed. Technically, the strand for the features in junctions.bed would be the same as if you were looking at the XS flag in the BAM file, so junctions.bed works very nicely now

cmdcolin commented 8 years ago

Given that, I'm tagging the first release of this plugin. Thanks for the suggestions @billzt :+1: