What does the seventh column of the inputted file represent?

[kuangzhuoran]

The first six columns represent the genomic positions, the eighth column should be the interaction counts, and the ninth column represents the p-values。
I don't quite understand the meaning of the seventh column.

what does 99179/ 99186/ 99175 mean
chr22 18312801 18313021 chr22 18558869 18559119 99179 105 0.000000
chr22 18941930 18942280 chr22 19132279 19132487 99186 8 0.032835

[kuangzhuoran]

Another question is, I'm wondering if the first three columns are the target or if it's the fourth to sixth columns? Taking ’example_data‘ as an example, is ‘example_loop_data.hg19.GM12878.bedpe’ the target?

[adadiehl]

Greetings, The example data files follow bedpe conventions. You are correct that the first six columns represent loop anchor loci: columns 1-3 represent the first loop anchor and 4-6 represent the second anchor. The seventh column is the name column, and contains a unique identifier for each loop. To expand more on terminology, I'm using 'query' and 'target' to differentiate between the two sets of loops used in a comparison. The query is the first sample in the comparison. All the loops in this sample are compared to loops in the query set, and will be labelled with their conservation class in the output. Hope this helps! Best, Adam Diehl

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On Tue, Mar 19, 2024 at 1:58 AM kuangzhuoran ***@***.***> wrote: Another question is, I'm wondering if the first three columns are the target or if it's the fourth to sixth columns? Taking ’example_data‘ as an example, is ‘example_loop_data.hg19.GM12878.bedpe’ the target? — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSOX4IKOJX4JNTI2BS3YY7HZLAVCNFSM6AAAAABE43ZSKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBVHAZTSOJYGI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kuangzhuoran]

Thanks for your help !