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genomeSAsparseD option for RSEM Star? #202

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Leelab-623 opened this issue Jul 25, 2023 · 0 comments
Open

genomeSAsparseD option for RSEM Star? #202

Leelab-623 opened this issue Jul 25, 2023 · 0 comments

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@Leelab-623
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Hi! My current pipeline involves STAR alignment to generate BAM files, then move to RSEM for quantification. However this pipeline is quite slow when RSEM reads the BAM file. I wanted to use the STAR packaged in RSEM, but due to the RAM limitation, I could not run RSEM without the --genomeSAsparseD 2 option. I wonder if there's any workaround with this issue? Thanks!
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