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openvax / neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Apache License 2.0
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Add argument to STAR to save unmapped RNA reads #126

Closed iskandr closed 5 years ago

iskandr commented 5 years ago

Our DNA alignment pipeline currently leaves both mapped and unmapped reads in the BAM. This makes it easier to later inspect the unmapped reads (e.g. were they viral?) and also lets us estimate the mapping rate directly from sambamba flagstat output.

STAR, on the other hand, drops unmapped reads from the output BAM by default.

To retain unmapped reads, this PR adds --outSAMunmapped Within to invocations of STAR.

Here's the STAR reference manual entry for this option:

--outSAMunmapped
  default: None
  string: output of unmapped reads in the SAM format
    None
      no output
    Within
      output unmapped reads within the main SAM file (i.e. Aligned.out.sam)
iskandr commented 5 years ago

@julia326 OK to merge?

julia326 commented 5 years ago

Could you add a PR description explaining this change and the expected effect?