Staden gap5 : Template Plot Colors

[sklages]

Hi,
in the gap5 template plot I see colors not mentioned in the manual (nor in the publication) and I was wondering about their meaning.
E.g. yellow, light green, dark green, magenta, "pale" yellow or "peach"(?), pink, different intensities cyan, light blueand maybe others I have overseen.


I have configured the template track to show "Template Size" and "Combined Mapping Quality". "Y-log-scale" and "Avg. Insert Size" are "ticked.


This is probably something obvious ... any hints?


thanks,
Sven

[jkbonfield]

The manual is in a desperate need of an overhaul!

The colours you are seeing are at the top of the template display, where the single-ended reads or contig spanning read-pairs sit? If so they are all spanning contigs with the colour *approximately* indicating which contig they are linking to. I say approximately because it's not a 1:1 mapping but a many_contigs to one colour mapping (given there are usual more contigs than the 10 or so colours we use).

Basically if you see a technicolour smear then it's probably a wide spread repeat. If you see a single block of spanning reads all of the same colour then it's likely a real link to one specific contig.

Edit: I see you're using the latest code with average insert sizes. Glad to hear it (and sorry we haven't released a proper tarball yet). Please do pass on any bugs you find to me directly. Cheers.

[sklages]

Thanks for your quick response.

I have attached an example screenshot; I still cannot figure out what the colored reads/template are showing ..

example: https://ws.molgen.mpg.de/ws/141031/tview.jpg

If I find any bugs I'll report them (unless I am the bug ;-) )

Sven

[jkbonfield]

Those look to me to be reads that are spanning two contigs. I assume you either have variable length reads or you're using the Y-Spread function to spread them out a bit (it helps a lot to see clusters when all your reads are identical size).

They look like they're clustering around gaps in the short read-pair library so I assume these are contigs ends which have been scaffolded or joined together with a longer (454?) library.

If you double click to bring up the editor at one of those spots with lots of coloured reads, eg the patch of yellow ones 2/3rds of the way along, and in the editor use Settings -> Group Readings By -> Template Status then you will see a bunch of orange labelled reads in the editor indicating contig spanning templates. If you click the first, shift-click the last to select them all and put in the "readings" list and then left-click the editor "Size: <num> -" button in the bar at the top (or use the Main window Lists -> Edit List) and "View multi-column" then you'll see all the reads you selected along with their pairs and which contigs they map to. You can then sort that display by Pair Position and then again by Pair Contig to get them arranged into clusters of where the pairs map to.

All this fiddly clicking *ought* to be doable directly from within the template display - eg just ring a bunch of reads with the mouse and get it to pop up a summary of what reads they are and what other contig regions are involved. However that's still to be written. :-)

James

[sklages]

Thanks for your comprehensive answer. Now I got it.

This is a contig from a denovo assembly of IlluminaPE100, PE454 and Pacbio reads.

And, as a side-effect, I learned how gap5 helps me in investigating read / contig pairing :-)