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Old 07-22-2019, 12:08 AM   #1
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Default Some basic questions about Seqmonk for Hi-C data


I am using Seqmonk for the first time and have some basic questions about hi-c data in general and about seqmonk.

I want to compare two conditions and have 2 biological and 2 technical replicates for each (total 8 bam files). Should I first merge the bam files of technical replicates before importing them into Seqmonk? I saw the Data Group function which can be used to group data but am a little unsure if that is appropriate for merging technical replicates?

Secondly, I want to identify interactions that show the statistically significant changes between the two conditions. For this I define probes with a resolution of 100k, quantitate them by read coverage and then use the edgeR filter. Since some pipelines also recommend merging all biological and technical replicates to increase hic coverage I was wondering which filter would be the best to identify significant changes in interactions in this unreplicated merged data?

PS:I am also having some trouble running out of memory because of the huge files and was wondering if anyone has any tips for that.

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