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I was running idr on rep1 and rep2 and found out some of the output for rep2 do not match the rep2 narrowPeak file.
I'm copying one of the offending line below. As you can see, the rep2 end location and summit info are not correct. While the rep1 info are correct. This makes me worry about the results. I'm hoping someone can respond. Thanks!
idr file: chr7 29413398 29416918 . 1000 . -1 213.82509 -1 2529 2.46 2.73 29413398 29416918 620.03809 2548 29413672 29416512 213.82509 702
and here is the associated peak in rep2 narrowPeak chr7 29413672 29414923 rep2 2138 . 20.03013 213.82509 209.88286 676
FYI, the associated peak in rep1 narrowPeak is correct. chr7 29413398 29416918 rep1 6200 . 25.59149 620.03809 615.40747 2548
The text was updated successfully, but these errors were encountered:
Ok. I may have found why the discrepancies.
The reason why I cannot find the rep2 peak with exactly the same location was because there are several rep2 peaks that overlap in this region. Although, I wasn't able the find exactly the same location (they are off by 7 bp) after merging all those rep2 peaks that overlap, I'm now thinking that this may not a bug as it may have some other overlapping peaks that I somehow missed.
I was running idr on rep1 and rep2 and found out some of the output for rep2 do not match the rep2 narrowPeak file.
I'm copying one of the offending line below. As you can see, the rep2 end location and summit info are not correct. While the rep1 info are correct. This makes me worry about the results. I'm hoping someone can respond. Thanks!
idr file:
chr7 29413398 29416918 . 1000 . -1 213.82509 -1 2529 2.46 2.73 29413398 29416918 620.03809 2548 29413672 29416512 213.82509 702
and here is the associated peak in rep2 narrowPeak
chr7 29413672 29414923 rep2 2138 . 20.03013 213.82509 209.88286 676
FYI, the associated peak in rep1 narrowPeak is correct.
chr7 29413398 29416918 rep1 6200 . 25.59149 620.03809 615.40747 2548
The text was updated successfully, but these errors were encountered: