pairtools
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open2c
Extract 3D contacts (.pairs) from sequencing alignments
currently not rendered & doesn't seem to link to proper multiqc or describe how to use it: suggestions?
Hiya, I've got the feeling that `chrU1` is a typo, and it should have been `chrU`. The change was made in [#117](https://github.com/open2c/pairtools/pull/117/files#diff-52ac73f774be95a098068c3b942c2c575e43ec45ad3b0848131313336cc8b750R25). Best, Matthieu
generate coverage in bedgraph/bigwig format with a given resolution from .pairs files. can be based on pairtools.filterbycov module. parameters to include: - resolution should be set up externally - output...
As suggested by @gfudenberg , let's add convergence point of the four orientations to stats!
Premise: - `pysam` is fast but introduces multiple logistic complications. We may want to replace it with manual bam parser (Anton's style). `pysam`: - is complicated to link in isolated...
Are pairtools supported on OSX? It's removed in a recent conda recipe. Why?
Pysam include library directory and set libraries instead of providing full path. Set rpath so libs are found when installed in a virtual environment or in user-space. This allow to...
#### Needs discussion/fix: - [ ] bam annotation? https://github.com/open2c/pairtools/issues/67 - [x] ~~report mapq in the stats: https://github.com/open2c/pairtools/issues/80 (or extend to any specified additional fields?)~~ This was actually implemented in the...
We used to have following fields in the stats before https://github.com/mirnylab/pairsamtools/commit/85ddfb309591cb0b8bea56130ca5648afeac77d6 ``` total_unmapped total_single_sided_mapped dedup/n_unmapped ``` Now after https://github.com/mirnylab/pairsamtools/commit/85ddfb309591cb0b8bea56130ca5648afeac77d6 we are collecting stats in the `dedup` step the same way,...
