(K) Conservation by phyloP (medium, needs A,I,J)

[mrshu]

• Based on multiple alignment from part J, find which positions are conserved in evolution (the result is a numerical level of conservation per position in a wiggle format)
• See tracks Align. Cons. (L) and Multiz. Cons. (L) in sacCer3 browser (here we want only one track)
• Use the same tree as in I
• https://github.com/fmfi-genomika/genomika-2017/wiki/PhyloP-tracks

[mrshu]

@ViRPo Anything I can help you with here?

[virpo]

@mrshu I am getting there, no hiccups yet I will try to finish it before our meetup, and if I have any problems, I will ask you there :)

[virpo]

I ran into an error, that I was not able to resolve after trying for an hour

I described what steps I took here: https://github.com/fmfi-genomika/genomikaMalGlo/wiki/PhyloP-tracks

Do you have any tips or have you seen it before? cc @mrshu @bbrejova

[Zygro]

Same in (L) #12

[virpo]

@Zygro I finally found how to resolve this! In my case, I had a single .maf file which contained multiple .maf files combined In order to make it work, I had to either split it into multiple separate files or just use .maf that is already split by other group located in /data/malSym/taskK/chrom_split/ I hope this helps

[virpo]

Alright, finally resolved all the issues

Documentation: https://github.com/fmfi-genomika/genomikaMalGlo/wiki/(K)-PhyloP-track