Question: Making chain files
2
gravatar for mc2548
5 weeks ago by
mc254810
mc254810 wrote:

I work on non-model insect genomes. In order to look for orthologous regions across species I have had been blasting in the past. But I needed something more robust. I used the online version of mVista and that has been helpful but was recently advised to use liftover. Realised that I needed chain files for the same. However, when I reached out to UCSC they said they cannot make chain files for invertebrate genomes. So any help in making chain files for liftover will be appreciated? Or any help in finding orthologos non-coding regions across species will be appreciated.

My problem more specifically: I am trying to find orthology/synteny of 200kb region across multiple species for which I have the ATAC peaks of in order to look for similar reg-regions.

ADD COMMENTlink modified 29 days ago by Biostar ♦♦ 20 • written 5 weeks ago by mc254810
1

Take a look at this: https://iamphioxus.org/tag/liftover/ It also has links for UCSC pages at the bottom of the post.

ADD REPLYlink written 5 weeks ago by genomax70k

From my understanding, this is for 2 different assemblies for the same reference genome/organism. How different will it be for 2 distant species?

ADD REPLYlink written 5 weeks ago by mc254810
1

No. There are chain files that go across species. e.g. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/

ADD REPLYlink written 5 weeks ago by genomax70k
1

I have used the pipeline from UCSC (http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl ). It is a bit tricky to install (especially the parasol job submission system from UCSC) but it works like a charm. Gives all types of chains including liftover chains. No root access is needed to install parasol and I found it easiest to run the pipeline with parasol rather than to modify it to run without it.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by microfuge1.2k

As you pointed out, I have been having trouble to install the parasol job submission system. This is where I downloaded it from: https://genecats.gi.ucsc.edu/eng/parasol.html but this does not look like what is described in here: http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system . Any help in downloading parasol and getting it to work will be appreciated

ADD REPLYlink written 5 weeks ago by mc254810

There is a direct script available to install it (http://genomewiki.ucsc.edu/images/e/ea/ParasolInstall.sh.txt ). It assumes a root access but can be modified easily to install somewhere else. It largely copies binaries from UCSC.

ADD REPLYlink written 4 weeks ago by microfuge1.2k
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