not generating unnecessary "fail" files from bam filtering

EichlerLab / isoseq_pipeline

Isoform detection with paralog-specific partitioning

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not generating unnecessary "fail" files from bam filtering #3

Closed mldough closed 7 years ago

mldough commented 7 years ago

Currently for each partition, when the master bam file is intersected with that partition's bed, a "reject" file is createdsamtools view -U. This results in many unnecessary files (each partition has its own reject bin). Better to remove -U and just run a final command for all regions so there is only one "reject" bin.

bnelsj commented 7 years ago

Fixed in ffd3bff76ef4c9cb231298b85469d334bb753ad9