SNP coordinates NOT in peak.

[tzhu-bio]

Hi, thanks for your excellent scripts.

I found the SNP coordinates not located in peak regions with my own data. But it seems normal with your example data.

[nikhilmilind]

Hello!

Which script are you executing? Is the script you are executing from the master branch or the python3 branch?

Also, which SNPs are you testing for overlap with your peaks?

[tzhu-bio]

Hello!

Which script are you executing? Is the script you are executing from the master branch or the python3 branch?

Also, which SNPs are you testing for overlap with your peaks?

Thanks for your reply. The above result was produced by the python 3.8 scripts.

Now I get the right result with the python2.

[nikhilmilind]

Ah so the picture you sent is the SNPsOverlappingPeaks.txt output from CHEERS_computeEnrichment.py? In that case, the file contains all the SNPs that overlap peaks. Are you saying that you were expecting no overlap to occur?

[tzhu-bio]

Ah so the picture you sent is the SNPsOverlappingPeaks.txt output from CHEERS_computeEnrichment.py?

Yes.

For the initial question, let me give you an example:

The SNP1 coordinate is chr1 10, but the SNPsOverlappingPeaks.txt return the SNP1 overlap with peak (chr1:100-300).

[nikhilmilind]

This is probably because your SNP positions or the start/end coordinates for the peaks are being interpretted as characters rather than integers. I would check to make sure that these columns contain only integer values.

I've added a quick fix on my fork of the repository (https://github.com/NMilind/CHEERS/blob/master/CHEERS_computeEnrichment.py). Would you mind testing it to see if it fixes your problem? If it works, I'll work to integrate it into this repository.

[tzhu-bio]

I'm very sorry to tell you that it still doesn't seem to work.

[nikhilmilind]

That is unfortunate - Would you be able to send me the files you are using as input to CHEERS_computeEnrichment.py? Just the top few lines from each file should work, as long as the error is reproducible with them.

[tzhu-bio]

trait_counts_normToMax_quantileNorm_euclideanNorm.txt
awn.txt

[nikhilmilind]

Excellent, I seem to have found the issue this time around. Would you please mind trying again? Here is the updated script: https://github.com/NMilind/CHEERS/blob/master/CHEERS_computeEnrichment.py

[tzhu-bio]

It's running successfully now, thanks for your patience and help.

[AnnaLorenc]

Good job, well done 😊 Ania From: Nikhil Milind ***@***.***> Reply-To: TrynkaLab/CHEERS ***@***.***> Date: Saturday, 21 May 2022 at 14:17 To: TrynkaLab/CHEERS ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [TrynkaLab/CHEERS] SNP coordinates NOT in peak. (Issue #2) [EXT] Excellent, I seem to have found the issue this time around. Would you please mind trying again? Here is the updated script: https://github.com/NMilind/CHEERS/blob/master/CHEERS_computeEnrichment.py [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_NMilind_CHEERS_blob_master_CHEERS-5FcomputeEnrichment.py&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=6vircarprbHSQKvgcPf4oNEQzuZv8X5fiEBES365mL8&m=tV7iwG6jvVwyu0oEozIac_mMsXGp67QDgvil7WzX6qmkkWGjXEqfp9uS659uKRex&s=pbOTCJg5DlDAfRjEmOd0SVYaC1eKRpo1GKgLrd2y2p8&e=> — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_TrynkaLab_CHEERS_issues_2-23issuecomment-2D1133632841&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=6vircarprbHSQKvgcPf4oNEQzuZv8X5fiEBES365mL8&m=tV7iwG6jvVwyu0oEozIac_mMsXGp67QDgvil7WzX6qmkkWGjXEqfp9uS659uKRex&s=9NrYnNkn6OMXQf7l0-5RmpRycnlV_9zEtnDutKjZOiI&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AMIP6C2I2BSMTH2WGIWTQKTVLDO6ZANCNFSM5WOBRAAA&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=6vircarprbHSQKvgcPf4oNEQzuZv8X5fiEBES365mL8&m=tV7iwG6jvVwyu0oEozIac_mMsXGp67QDgvil7WzX6qmkkWGjXEqfp9uS659uKRex&s=BUHSVj6sSDiL6bTxOYy3R13WP1-BsJK13NYUmZGYTNM&e=>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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