Error: could not find chromosome: at lib/Regulome/RegulomeDB.pm line 294.

[Niladri-B]

Hei,

I have a list of dbSNPs for specific regions of the genome that I am trying to get info and data on. However, I keep getting the aforementioned error for 3 such regions in my dataset.

Would it be possible to identify the possible causes for this error? I can give more details if need be(e.g the regions I am facing the problem)

Thanks and I look forward to your response.

[hitz]

This error occurs when RegulomeDB cannot find the SNP by dbSNPid. This can happen if your snps are from a later version of dbSNP that ours (141)

[Niladri-B]

Hei and many thanks for the quick response!

I will try to find out which version of dbSNPs my SNPs belong to. What puzzles me a bit though is why I get this error only in 3 specific regions.

Perhaps these 3 regions have snp names that are different from what is in the regulome database?

[Niladri-B]

Hi again,

I have now confirmed that my snps seem to belong to dbSNP 142.
Is there any way to convert them back to the old build of 141?

Do you think this is a good tool?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704719/

[hitz]

I have never used that tool so I cannot vouch for it. I think what you would need to do is get the coordinates for the SNPs that aren't in 141 and submit those without a SNP ID. Pretty sure you want the hg19/GRCh37 coordinates. Ben

…

On Oct 10, 2017, at 3:29 AM, Niladri-B ***@***.***> wrote: Hi again, I have now confirmed that my snps seem to belong to dbSNP 142. Is there any way to convert them back to the old build of 141? Do you think this is a good tool? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704719/ — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

-- Benjamin C. Hitz ENCODE DCC * Dept. of Genetics hitz@stanford.edu

[Niladri-B]

Oh you mean I don't really need the rsIDs? Wow...well then I'll try to put just the coordinates in as I have coordinate info for all of my SNPs in hg19 yes.

[Niladri-B]

Hi again!

So now I used the chr position info and it worked.

However, I am getting different results based on whether I use dbSNP ids (for the regions where there wasn't a problem) vs using coordinates.

For example, in one of my regions, using dbSNP gives hits as high as 1b while in the same region using chr coordinates is giving only 2b.

What could be the reason and which result should I follow along?