Regarding PhestCons and phyloCSF

[Pritesh Sabara]

Hi,

I am working with lncRNA prdiction of Bos taurus (BosTau8).

I want to create PhastCons score file for use in lncRScan-SVM tool as well as I also want to predict coding potential of some lncRNA which I have found using cuffcompare and extracted in fasta sequences through PhyloCSF. I want your help, if you can guide me how to create  MAF fasta file to input in PhyloCSF.

Thank you.

Good day.

Dr. PRITESH SABARA

Research Associate

Department of Animal Biotechnology

College of Veterinary Science and Animal Husbandry

Anand Agricultural University

Anand  

M-09427216099

[Jairo Navarro Gonzalez]

Hello Pritesh,

Thank you for using the UCSC Genome Browser and your inquiry. I must apologize for sending the wrong response to your question previously. 

Unfortunately, we do not have enough information to help create your MAF, such as the other species you want inside your MAF. However, our engineers share if you are starting from scratch, you may find the following wiki page useful to create your pairwise alignments:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

Our makeDb/doc/* files have many examples of how to run multiz and phastCons on a few species. For example, bosTau4.txt shows the steps that one of our engineers followed to make a 5-species multiz:

https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/bosTau4.txt#L606

and phastCons:

https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/bosTau4.txt#L1101

It's not light reading, but it does show the input parameters and command lines used. You may find this previously answered question helpful:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Ne1MFN6Sy_8/r6vuVDUtAQAJ

If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro 
UCSC Genome Browser

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