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-#To do:
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-#- polyA trimming for 3' data
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-#- update dataset to have better base qualities
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-#- add potential handling for rsem quantification after hisat alignment (would require getting a transcriptome alignment from hisat)
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-# confirm why picard_rrna list needs to be different for hisat
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#####~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# setup environment
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