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rr1859 / R.4Cker

MIT License
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cis analysis does not agree with the bedGraph #25

Open iprada opened 7 years ago

iprada commented 7 years ago

Hi,

I have run my analysis on far cis and 4C-ker didn't raise any warning. When I did upload my track to the UCSC genome browser for visualizing my results and compared them to the input bedGraph, I noticed that there is almost no overlap between the elements in the bedgraph file vs the elements in the bed file of the interacting sites. Could you please let me know what could be going wrong?

Also, what concerns me is that there are some regions that are called as interacting sites even though there are no reads supporting the interaction in that genomic region.

I am working with the following data files:

-The one identified by 4C-ker as high interacting in cis -The bedgraph of the reads aligned to the reference genome hg19

Please, find attached a screenshot of the genome browser addressing this problem

genome_browser

rr1859 commented 7 years ago

How far is this from your bait and what value of k did you use? Im assuming something went wrong with the parameter estimation.

iprada commented 7 years ago

I did use different values of k (5,6 and 11) to asses if this was caused by the value of k. I see this pattern around all the chromosome. The software did not claim on anything about the parameter estimation. If required, I could provide you the bedgraph file and the session info by private.

rr1859 commented 7 years ago

Sure please send it.

ajinkya-deogade commented 5 years ago

Hi, I am also observing the same issue. The high and low interacting domains are swapped. I have tried different values of k. Increasing k improves the correspondence between bedgraph and the domains but super high interacting domains are dropped.

As suggested by you, it seems there is a problem in parameter estimation. I don't know how can I improve the parameter estimation other than tweaking the value of k. What can I do?