leafcutter
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leafcutter_cluster_regtools and "?" stranded regtools junc files
This has been noted by at least one user in a private email to me.
Using regtools on the suggested parameters for unstranded libraries ( -s=0), regtools occasionally reports junctions with "?" in the strand field. For one user, this amounted to 22 junctions out of 285,000 so I'm happy for these junctions to be ignored.
This shouldn't be an issue when regtools is used with stranding parameters (-s=1 or -s=2).
I'll make up a pull request to leafcutter_cluster_regtools to ignore lines with "?" in the strand column.