phastCons conservation scores for Humans

[Debadeep Chaudhury]

Dear Sir/Ma'am,

    I'm trying to retrieve the conservation scores of bases between Humans, Chimps and Rhesus Macaques to use in my evolutionary analysis of the species. I managed to obtain a multiple-alignment between the 3 species but I'm stumped at the step of generating the phastCons track from this file.

    I'm writing to inquire whether the 19way or 30way conservation tracks available on UCSC provide adequate information on the conservation between the aforementioned 3 species or if it's more accurate to calculate it de-novo.

    In the case of the latter scenario, if calculation of the phastCons scores for Humans, Chimps and Rhesus would be the better way to go, I would be extremely grateful if you could guide me towards generating the dataset reliably. Thank you and I'll look forward to your reply.

With best regards,

Debadeep Chaudhury

Doctoral Student

Dioscuri Center for Chromatin Biology and Epigenomics

Nencki Institute of Experimental Biology

Polish Academy of Sciences (PAN)

Warsaw, Poland

Email: d.cha...@nencki.edu.pl

Tel: +48 22 58 92 488

https://www.nencki.edu.pl

[Daniel Schmelter]

Hello Debadeep,

Thank you for your email to Genome Browser support and for your patience with this longer-than-usual delay in response. 

I cannot comment on the adequacy of any alignment tool for any particular application. Your research may have special requirements and the best way to determine if any component is accurate is to read more from the original authors. I can say that the datasets and alignment tools we use are high-quality and are widely used. Congratulations on running a multiple alignment successfully between those three species. Running a PhastCons scoring is outside of the scope of what I can instruct, but I will direct you to their website.

http://compgen.cshl.edu/phast/help-pages/phastCons.txt

You can see how we make such data tracks from our makeDoc, here is our 27-way alignment. The phastCons parts start on line 1075:

https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/multiz27way.txt

Both of these sources are relatively dense and might be difficult to read or consume. The first thing I'd recommend is reviewing the track description for PhastCons. I'd also review the visual display of conservation tracks in general. Here is a session with some relevant tracks turned on, highlighting your species. 

https://genome.ucsc.edu/s/dschmelt/hg38.chimp.rhesus.align

I hope this was helpful. If you have any more questions, please reply-all to our public support email at gen...@soe.ucsc.edu. For private communication, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter

UCSC Genome Browser; UCSC Genomics Institute
Twitter | Facebook | YouTube

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAM5kHY_68411bgup4V3KjUk290G8wVq%2Bs%3D9OU0wnb6Tu7NwVSQ%40mail.gmail.com.