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change STAR outSAMunmapped argument #433

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hbeale opened this issue Sep 6, 2016 · 0 comments
Open

change STAR outSAMunmapped argument #433

hbeale opened this issue Sep 6, 2016 · 0 comments

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@hbeale
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hbeale commented Sep 6, 2016

The bam file is created by the RNA-Seq pipeline omits some reads in the output, which chokes our duplicate-finder. In the STAR params in aligners.py, the current outSAMunmapped argument is "Within", but needs to be "Within KeepPairs"
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