python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BMMC_single_donor_ATAC_L001_R1.fastq.gz BMMC_single_donor_ATAC_L001_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq-barcode-annotate.py R1_human_barcodes.txt 0 65 8 R2_human_barcodes.txt 0 103 8 R3_human_barcodes.txt 0 141 8 -R2barcodes 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - BMMC_single_donor_ATAC_L001.barcodes_annotated; gzip BMMC_single_donor_ATAC_L001.barcodes_annotated.end*.fastq
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BMMC_single_donor_ATAC_L002_R1.fastq.gz BMMC_single_donor_ATAC_L002_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq-barcode-annotate.py R1_human_barcodes.txt 0 65 8 R2_human_barcodes.txt 0 103 8 R3_human_barcodes.txt 0 141 8 -R2barcodes 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - BMMC_single_donor_ATAC_L002.barcodes_annotated; gzip BMMC_single_donor_ATAC_L002.barcodes_annotated.end*.fastq
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BMMC_single_donor_RNA_L001_R1.fastq.gz BMMC_single_donor_RNA_L001_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq-barcode-annotate.py R1_human_barcodes.txt 0 65 8 R2_human_barcodes.txt 0 103 8 R3_human_barcodes.txt 0 141 8 -R2barcodes 40 -addUMI 2 40 10 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - BMMC_single_donor_RNA_L001.barcodes_annotated.UMI; gzip BMMC_single_donor_RNA_L001.barcodes_annotated.UMI.end*.fastq
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BMMC_single_donor_RNA_L002_R1.fastq.gz BMMC_single_donor_RNA_L002_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq-barcode-annotate.py R1_human_barcodes.txt 0 65 8 R2_human_barcodes.txt 0 103 8 R3_human_barcodes.txt 0 141 8 -R2barcodes 40 -addUMI 2 40 10 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - BMMC_single_donor_RNA_L002.barcodes_annotated.UMI; gzip BMMC_single_donor_RNA_L002.barcodes_annotated.UMI.end*.fastq