Matthew DeMaere
Matthew DeMaere
bin3C imposes on the user that input BAMs are query name sorted. This makes pair matching trivial and low memory. However, when it comes to invoking `bin3C extract -f bam...
Currently `bin3C extract` assumes that a single BAM file backs the contact map instance. When `bin3C combine` is used to merge maps made from separate `bin3C mkmap` calls, this is...
Each command as a set of required input files. Some analysis stages are long-running and we should test for all files immediately at invocation, so that users don't find out...
Add to documentation the importance of cleaning up hi-c reads used in creating the contact. This can be accomplished with tools such as bbduk. In particular cleanup should remove leading...
Problem sizes can be very large and bin3C does not offer any sort of guidance to end-users on what sort of resource requires will be need to analyze their dataset...
A sub-command which invokes the full workflow would be user friendly and easy to implement.
As of now, if a user invokes bin3C second stage for a different location from where the map was created, the relative paths can mean bin3C might look in the...
When using the Docker image within Singularity, invoking tradis_merge_plots produces the error: ```shell sh: 1: tradisfind: not found ``` This is not surprising as I cannot find an instance of...