python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py The_musk_gland_Single-Nucleus_ATAC-Seq-GSM5518345-all.end1.fastq.gz The_musk_gland_Single-Nucleus_ATAC-Seq-GSM5518345-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - The_musk_gland_Single-Nucleus_ATAC-Seq-GSM5518345-all.2x36mers.Moschus_berezovskii-ls35.final.genome_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py The_musk_gland-Single-Nucleus_ATAC-Seq_3-GSM7163853-all.end1.fastq.gz The_musk_gland-Single-Nucleus_ATAC-Seq_3-GSM7163853-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - The_musk_gland-Single-Nucleus_ATAC-Seq_3-GSM7163853-all.2x36mers.Moschus_berezovskii-ls35.final.genome_HiC.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py The_musk_gland-Single-Nucleus_ATAC-Seq_4-GSM7163855-all.end1.fastq.gz The_musk_gland-Single-Nucleus_ATAC-Seq_4-GSM7163855-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Moschus_berezovskii-ls35.final.genome_HiC-DNAZoo/bowtie-indexes/Moschus_berezovskii-ls35.final.genome_HiC.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - The_musk_gland-Single-Nucleus_ATAC-Seq_4-GSM7163855-all.2x36mers.Moschus_berezovskii-ls35.final.genome_HiC.unique