(E) Augustus (slow, needs A)

fmfi-genomika / genomikaMalGlo

Malassezia globosa

0 stars 0 forks source link

(E) Augustus (slow, needs A) #5

Closed mrshu closed 6 years ago

mrshu commented 6 years ago

Run gene finder Augustus, create track with predicted genes (for comparison with annotation)
Download and install software from http://bioinf.uni-greifswald.de/augustus/
- Already installed on compbio servers
Example of command line: augustus --uniqueGeneId=true --species=ustilago_maydis genome.fa > augustus.gtf
ustilago_maydis is a related fungal species used for training parameters
The result needs to be converted from gtf to genepred, by gtfToGenePred (at genomika server) with option -genePredExt
If you name your track augustus, genome browser will recognize it automatically, no need to modify trackDb.ra

mrshu commented 6 years ago

@Zygro anything I can help with here (so that we can close this)?

mrshu commented 6 years ago

@Zygro Please let me know if I can help in any way to get this done.

Thanks!

Zygro commented 6 years ago

@mrshu I didn't get enough time to do this, but i should be able to do it this weekend

Zygro commented 6 years ago

I have the data, however I can't find where is the DB. MalSym wiki says that I should run hgLoadGenePred -genePredExt malSym1 augustus augustus.genePredExt, however I have no idea in which directory as I generally get can't find database malGlo1 in hg.conf, should have a default named "db"

mrshu commented 6 years ago

@Zygro just out of curiosity, did you follow this guide in order to set up your environment?

https://github.com/fmfi-genomika/genomika-2017/wiki/Basics-of-creating-tracks#getting-access-to-mysql

I guess it may help a bit =)

Zygro commented 6 years ago

done that, track is now online