agalitsyna

Hi, Kim! This usually means that the matrix is too sparse for balancing at this resolution, and rows/columns of Hi-C matrix have too little counts for balancing. Before confirming that,...

Yes, in Drosophila and other insects we usually call compartments in cis and per chromosome arms. Otherwise they are too dominated by Rabl configuration. I also use fine resolution, far...

Hi, Alena @taskina-alena, cooler cload creates a single matrix when run with -N parameter. Here is an example: `cooler cload pairs --no-symmetric-upper genomic_bins.bed pairs.tsv output.cool` However, I'm not sure I...

@Phlya Can you provide no_filter stats and full stats file, please?

I suggest checking G1_DMSO_rep2.no_filter.hg38.stats.txt against G1_DMSO_rep2.hg38.stats.txt, not G1_DMSO_rep2.mapq_30.hg38.stats.txt

by the way, the total number of reads is inevitably reduced with mapq30 filter, because `pairtools select '(mapq1>=30) and (mapq2>=30)'` will remove the pairs that have at least one segment...

Can you think of the script or pairtools command that will do what you expect to have in filtered stats then? Maybe marking all the filtered read instead of filtering...

Hi, @Phlya Thanks I think the only important thing to check is convergence of no_filter stats against the default output of distiller stats. Then it means that the pairs merging...

Thanks, cool! Interesting counterintuitive thing from your amazing stats: mapq_30 filter results in non-zero "total_unmapped". How come the read can have mapq>30 if it is not mapped? mapq is `bwa...

Hi, this is not the problem for MiSeq small reads only. In methods like Hi-CO (https://doi.org/10.1016/j.cell.2018.12.014) the length of meaningful read parts is required to be 15-36 bp due to...