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Hope everyone is well.

So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked of me, and what he gave me as primary data.

So he gave me 4 bed files (human genome) with chr and coordinates(start/stop), and asked me to do: "sequencing/coordinates conservation between diverse species".

Is that doable with coordinates only or do i need sequences in fasta format (phast uses fasta format)? I just dont understand how i will find "conservation between diverse species" only with coordinates. It seems weird to me.

I have found these programs: TargetOrtho2, Phast and BUSCO(?). Are they any good? Should i continue with one of them that you may have experience with?

Thanks

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    $\begingroup$ It is indeed a very unclear task. Are all the 4 bed files human bed files? What distant species you are interested in? $\endgroup$
    – Kamil S Jaron
    Apr 8 '20 at 11:55
  • $\begingroup$ Hi @JimHat That is cryptic, I think you need clarification! Literally that means non-humans. $\endgroup$
    – M__
    Apr 8 '20 at 13:04
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    $\begingroup$ I would suggest looking at those BED regions in the UCSC 100-way conservation tracks. Just doing that might just suffice. $\endgroup$
    – Devon Ryan
    Apr 8 '20 at 21:11
  • $\begingroup$ hi all, and thanks for the answers! @KamilSJaron, yes they are bed files. He didnt clarify which distant species but i am guessing species that represent some taxonomy (or sub catergory of one, also maybe a model organism). $\endgroup$
    – Jim Hat
    Apr 20 '20 at 10:21
  • $\begingroup$ @DevonRyan i wll try that. Thanks $\endgroup$
    – Jim Hat
    Apr 20 '20 at 10:22
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I second commenter Devon Ryan's suggestion, I'm just going to give a little more detail about how to do that. You can plug the BED files into the UCSC browser following these instructions: https://genome.ucsc.edu/goldenPath/help/customTrack.html

Now you can look at the overlap between your bed tracks (black boxes I believe) and conservation (red box).

enter image description here

Assuming that is all you want to do, that should do it. If you want to do further data analysis or processing, you can download the conservation track as a .wib file from UCSC. You can convert this file to BED as described here, and use BEDTools to analyze it together with your BED of regions of interest.

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  • $\begingroup$ Hi and thanks for the answer. By doing this, i will find whatever correlation there is between these bed files (which by doing what you suggested i will find the regions that are conserved(?) ) and -some- diverse species with bedtools? $\endgroup$
    – Jim Hat
    Apr 20 '20 at 10:27
  • $\begingroup$ Hi @JimHat, it is a little hard to tell exactly what it is that you are supposed to do based on the question, the simple answer is "yes", you will look for overlaps between conserved regions and your regions of interest using commands like bedtools intersect. But I don't have a clear idea of what your goals are beyond that. Also, I looked a little deeper and the browser doesn't have BED files of the conserved regions but it does have .wib files, which can yield bed files. See updated answer. $\endgroup$ Apr 20 '20 at 16:48

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