(J) Multiple whole-genome alignment (slow, needs A from both groups, I)

[mrshu]

• The goal of this track is to create a whole-genome multiple alignment of several genomes
• Use genomes from part I as well as malGlo and malSym genomes from the browser
• Beware that malSym1 and malGlo1 should be correctly named, both the genome as a whole and their chromosomes as in the browser
• The task requires some preprocessing - renaming things etc (fast), alignment computation (slow, we recommend running on compbio servers) and postprocessing (fast/medium)
  • Preprocessing and possibly also part of running alignment can be reused between groups - collaborate
• The notes from the last year consist of three parts: general introduction, Brona's notes (Example of use of tba in a different project), and student notes (Example of use of tba in a our project, display alignments).
  • Probably follow student notes.
  • The notes are not finished (end with "track does not work"), but the track was finished, see track "S. -Align (L)" in sacCer3 browser. See final version of sacCer3 trackDb.ra on genomika server.
• To run alignment, you need phylogenetic tree of these species. Use the tree from paper by Wu et al 2015 [4] - our species are in group B. Write the tree in the parenthesis notation
• https://github.com/fmfi-genomika/genomika-2017/wiki/Alignments

[matuszelenak]

I managed to do everything apart from the loading to the database (it seems). When I look into the malGlo1 database, there is a table (malGloMultAlignLocal) that contains the required data. How do I go around making them present in the browser? Do I have to just run that magic makefile now?

[mrshu]

@matuszelenak as far as I understand it, it should be just a matter of adding the track to trackDb.ra (in our case it is located in /kentsrc/trackDb/malGlo/malGlo1/trackDb.ra.

Looking at the task description, specifically at

The notes are not finished (end with "track does not work"), but the track was finished, see track "S. -Align (L)" in sacCer3 browser. See final version of sacCer3 trackDb.ra on genomika server.

it should be something on the order of

track sacCerMultAlignLocal2
shortLabel S. Align (L)
longLabel Saccer Alignment (Local)
group compGeno
speciesOrder sacCer3 sacPar sacMik sacKud sacArb sacEub sacUva
visibility dense
color 0,0,255
type wigMaf
viewLimits 0:1
autoScale off
maxHeightPixels 50:50:11
html sacCerMultAlignLocal2

(I got this from the sacCer/sacCer3/trackDb.ra file on the server).

Do let me know if that helps.

Thanks!

[mrshu]

Oh, and after the track is added, just run make alpha in /kentsrc/trackDb.

[vidriduch]

@mrshu @matuszelenak just to confirm it is exactly like mrshu described. Just add new track to trackDb.ra file and run make alpha. Few remarks regarding track configuration and what some of the fields mean. track describes what table the data are in so it should be something like track malGloMultAlignLocal. Short label is a visible text on top of your track. Long label is a tooltip text when you hover over the track and is also shown in the description page. Group defines in which part of the bottom page track will be in. Lastly, visibility defines what will be default settings of your track. These ones I figured out others are usually specific to the track. Hope this helps.

[matuszelenak]

Okay, your suggestions worked but the track in the browser is empty :( Guess there's the same problem which occured last year.

[tvinar]

Zjavne dokumentácia z minulého roku ohľadom tejto issue je menej ako dostačujúca.

Niekoľko otázok:

• Ako by z toho, čo sa nachádza v databáze a trackDb mohol browser vedieť, kde má hľadať zarovnanie? Je zarovnanie prístupné v adresári /gbdb kde majú byť všetky dôležité súbory? (a rozhodne všetky, ktoré má browser používať)
• Ako sa porovná to čo je v príslušnej tabuľke v databáze malGlo1 a v databáze sacCer3? V sacCer3 máte k dispozícii dva podobné tracky, jeden multiz7way (ktorý vyrobili ľudia v UCSC) a jeden, ktorý citoval Marek vyššie, ktorý vyrobili vaši kolegovia minulého roku
• Dokumentácia k minuloročnému tracku je síce strohá a nepresná, ale existuje ešte dokumentácia ku trackom v sacCer3, ktoré vyrobili ľudia v UCSC: /kentsrc/kent/src/hg/makeDb/doc/sacCer3.txt

[mrshu]

@matuszelenak Let me know if I can help push this forward in any way.

Thanks!

[bbrejova]

I do not see documentation on the wiki (how this track was created). Plus on today's meeting of the malSym group, we have discovered a small problem with the alignments in the browser - the reference species should not be in the list of the species in the trackDb.ra file, otherwise the server times out when a user clicks on the alignment. Ask @rasto2211 for details. Also I do not like very much the title "MG Align", the UCSC usually uses title "Multiz Alignment" for these tracks.

[mrshu]

Just FYI: I could not find a wiki for this task, so I created one here: https://github.com/fmfi-genomika/genomikaMalGlo/wiki/Multiple-whole-genome-alignment

[rasto2211]

It seems there is some problem with the ordering in the maf file with MSA and it causes some problem in the task L (#12).

[Zygro]

any progress?

[virpo]

@Zygro Matus just managed to redo the task J New MAF file is located in /gbdb/malGlo1/malGloMultAlignLocal/ and it worked for me, so give it a try as well