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!
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!