python ~/code/single-cell-RNA-seq/sciRNA-seq_counts.py L299-STAR-middle36mers-R2/STAR-2.5.3aAligned.sortedByCoord.out.bam Undetermined_R1_001.fastq.gz RT_indexes PCR_i7 PCR_i5 8 10 50000 /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/refFlat.hg38+mm10.annotation.renamed.gtf ~/genomes/hg38+mm10/hg38+mm10.chrom.sizes sci-counts.L299-STAR-middle36mers-R2-refFlat.exp50K -refFlat -UMIedit 2 -RTedit 1
python ~/code/single-cell-RNA-seq/sciRNA-seq_counts.py L299-STAR-middle36mers-R2/STAR-2.5.3aAligned.sortedByCoord.out.bam Undetermined_R1_001.fastq.gz RT_indexes PCR_i7 PCR_i5 8 10 50000 /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/gencode.v26+vm4.annotation.renamed.gtf ~/genomes/hg38+mm10/hg38+mm10.chrom.sizes sci-counts.L299-STAR-middle36mers-R2-GENCODE.exp50K -refFlat -UMIedit 2 -RTedit 1
python ~/code/single-cell-RNA-seq/sciRNA-seq_counts.py L299-STAR-middle36mers-R2/STAR-2.5.3aAligned.sortedByCoord.out.bam Undetermined_R1_001.fastq.gz RT_indexes PCR_i7 PCR_i5 8 10 35000 /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/refFlat.hg38+mm10.annotation.renamed.gtf ~/genomes/hg38+mm10/hg38+mm10.chrom.sizes sci-counts.L299-STAR-middle36mers-R2-refFlat.exp35K -refFlat -UMIedit 2 -RTedit 1
python ~/code/single-cell-RNA-seq/sciRNA-seq_counts.py L299-STAR-middle36mers-R2/STAR-2.5.3aAligned.sortedByCoord.out.bam Undetermined_R1_001.fastq.gz RT_indexes PCR_i7 PCR_i5 8 10 35000 /oak/stanford/groups/akundaje/marinovg/genomes/hg38+mm10/gencode.v26+vm4.annotation.renamed.gtf ~/genomes/hg38+mm10/hg38+mm10.chrom.sizes sci-counts.L299-STAR-middle36mers-R2-GENCODE.exp35K -refFlat -UMIedit 2 -RTedit 1