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4dn-dcic / pairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
MIT License
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Which coordinates does pairix return? #70

Open gdolsten opened 2 years ago

gdolsten commented 2 years ago

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 commented 2 years ago

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

gdolsten commented 2 years ago

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 commented 2 years ago

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?

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.

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