Which coordinates does pairix return?

[gdolsten]

For example, let's say the .pairs output is:

READID chrX 16145203 chrX 16213822 + - UU

Is 16145203 the left-most or the right-most coordinate on this read? Likewise for 16213822? Does this change based on the strand?

[SooLee]

I think it's the 5'end of the read, but the pairs format itself does not require it to be.

[gdolsten]

Ok, so for the "chrX 16213822" then the actual read would extend from <16213822 to 16213822, since it is negative stranded, so the 5'end would have the highest number in terms of genomic coordinates? Would it be possible to get confirmation on this? I was hoping to make an analysis based on these ideas and so these questions are very useful.

[SooLee]

It depends on how the file was generated. e.g. https://github.com/4dn-dcic/pairix/blob/master/util/bam2pairs/README.md#usage this utility has two options (5'end is default but could also use leftmost). Where did you get tgese pairs files?

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On Sun, Aug 8, 2021, 7:04 PM gabedolpten ***@***.***> wrote: Ok, so for the "chrX 16213822" then the actual read would extend from <16213822 to 16213822, since it is negative stranded, so the 5'end would have the highest number in terms of genomic coordinates? Would it be possible to get confirmation on this? I was hoping to make an analysis based on these ideas and so these questions are very useful. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#70 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHLO3DTY5E64RNJXFIVX7LT34LPNANCNFSM5BWUFYWQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .