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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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Run STAR in "two pass mode" to detect novel splice junctions #122

Open iskandr opened 6 years ago

iskandr commented 6 years ago

Add --twopassMode Basic option to STAR (https://ycl6.gitbooks.io/rna-seq-data-analysis/mapping_with_star.html)

We might also make this optional via the config file, since two-pass mode increases RNA alignment time.