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UCSC-Treehouse / pipelines

Makefiles to run dockerized pipelines used in Treehouse on a single sample
Apache License 2.0
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fusion-generated bams should also go into primary/derived #24

Closed e-t-k closed 5 years ago

e-t-k commented 5 years ago

22 was incomplete. also need to move bams generated from the fusion step ( I didn't realize these existed) into primary/derived.

Filenames are FusionInspector.junction_reads.bam, FusionInspector.spanning_reads.bam & are directly in the fusion output dir.

e-t-k commented 5 years ago

Also include FusionInspector.fa and possibly but probably not FusionInspector.bed. see https://github.com/UCSC-Treehouse/operations/issues/276 . Edit: leave these in downstream per https://github.com/UCSC-Treehouse/operations/issues/276#issuecomment-458243594