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some questions #66
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Thank you, I have one more question, Suppose I train with odd chr and test with even chr. Suppose I test with chr 8 which has in the contacts.gz file, it has 1013818 loops the output ".scc" which has original loops vs predicted ones to calculate the SCC value, this file has 324531 loops only. Is it expected to predict this less number of loops? If expected, what is the reason? if not expected, what can be the mistake that I did in running the program? Thanks a lot |
It happens because we predicted only contacts with the distance between loci less than 1.5 Mb. The contacts.gz file consists all contacts of the chromosome including long-range contacts.
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С уважением,
Полина Белокопытова
PhD student, NSU, Department of natural science, Genetics
Genomic Mechanisms of Development group
ICG SB RAS
Вторник, 20 июня 2023, 9:26 +07:00 от ahmedabbas811 ***@***.***>:
Thank you,
I have one more question,
Suppose I train with odd chr and test with even chr. Suppose I test with chr 8 which has in the contacts.gz file, it has 1013818 loops
the output ".scc" which has original loops vs predicted ones to calculate the SCC value, this file has 324531 loops only. Is it expected to predict this less number of loops? If expected, what is the reason? if not expected, what can be the mistake that I did in running the program?
Thanks a lot
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Dear all,
Why the predicted and real contact frequencies in the '.scc' file are too small (~0.0001)?
And how can I get values like the original values in the contact.gz files?
Thanks
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