voila visualization, tsv content

[myhoan...@gmail.com]

Hi everyone,

I have several questions regarding visualization on voila and content of tsv file.

1. In the doc attached, there are screenshots (Pic 1& 2) of the tsv file shown in the video tutorial. Compared to that tsv file, the tsv file i generated lacks the following columns: Gene ID, De novo junction, chr, strand. 

I was wondering what causes those missing columns? (maybe different majiq versions, or do you actually need to manually create those columns, or did my build/dpsi/voila commands lack any component critical to creating those columns?)

And if I want to retrieve those info, what should I do?

2. I'm comparing splicing of 2 groups: myoblast (group 1) and myotube (group 2). When visualizing result with voila on server (Pic 3), I can see the splice graphs of 2 groups, but not sure which one is group 1 and which one is group 2. Is the graph on the top always group 1, and graph at the bottom group 2, or is it the other way round? 

( there's labelling for myotube sandwiched between the 2 graphs, but no labelling for myoblast)

Thank you in advance for your help!

My

[Paul Jewell]

Hi My,

For 1) Which TSV file are you using? There is one generated when running majiq psi/dpsi, and a more comprehansive one generated when running voila tsv , can you verify which you were looking at? Also, some of the column headers have changed in very recent versions of voila. 

for 2), In the screenshot, it looks like the bottom plot is myotube. You can see the upped plot (myoblast) presumably by scrolling up on the pane with the splicegraph. You can also see more information about the chosen splicegraphs to display by clicking on the "Splice Graph" text / button at the very top of the page. 

Let me know if this helps, 

Thanks, 

-Paul

[My Hoang]

Hi Paul,

Thank you for your message!

For 1) I think I'm looking at the one generated during majiq psi/dpsi, since its name is "myoblast_myotube_dpsi", and it's located is in <dpsi_outdir>

(for 

majiq deltapsi -grp1 <build outdir>/<cond1_rep1>.majiq [<build outdir>/<cond1_rep2>.majiq ...] -grp2 <build outdir>/<cond2_rep1>.majiq [<build outdir>/<cond2_rep2>.majiq ...] -j NT -o <dpsi outdir> -n <cond1_id> <cond2_id>)

If the one above is actually dpsi tsv file, I guess I can check the voila tsv file. 

The linux machine I usually use for majiq crashed, so now I only have my windows laptop and an external drive which contains all the majiq data (bam, build files, dpsi files). 

Given my current situation, if I want to view the voila tsv file, what are my options? Do I need to install majiq + voila again on my personal laptop, or is downloading the Voila app enough? 

(I dont know if Voila app offers the choice to view Voila tsv file)

3) Just wonder if there exist an output file which tells the total number of novel splicing in my dataset? 

Thank you again!

My