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scottzijiezhang / MeRIPtools

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Issue with Bin Size #10

Open helen-zhu opened 3 years ago

helen-zhu commented 3 years ago

Hi Scott, Great paper. There seems to be an issue with the software, particularly the way that it assigns bins for peaks and retrieves peak coordinates aren't consistent.

Particularly, in counting reads, there's this line of code: slidingStart= round(seq(from = binSize/2, to = (exon.length - binSize/2), length.out = ceiling(exon.length/binSize) ) )

where the length.out <= binSize.

However in .getPeakBins:

mapping = data.frame(start = RNA2DNA[slidingStarts[1] - binSize/2 +1], end = RNA2DNA[slidingStarts[2] + binSize/2 ] )

which extends every peak index to +/- BinSize/2 which isn't consistent with the original assignment.

Would love to see an update on this.

Thanks, Helen

scottzijiezhang commented 3 years ago

Hi Helen,

Thanks for pointing out!

I have updated the bin slicing formula in a new version. Now, we make 3' end of each gene the elastic bin (larger than bin-size smaller than 2x bin-size) to accommodate the extra nt of a gene. This way, we will have exact bin size for most of the bin and have consistent location when retrieving genomic location of the bin.

Let me know if you have further suggestions.

Scott