python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R2-SRR3337493-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_nn_R2-SRR3337493-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R3-SRR3337494-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_nn_R3-SRR3337494-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R1-SRR3337495-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_DS_R1-SRR3337495-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R2-SRR3337496-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_DS_R2-SRR3337496-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R3-SRR3337497-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_DS_R3-SRR3337497-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R1-SRR3337498-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_nn_R1-SRR3337498-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R1-SRR3337500-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_16C_R1-SRR3337500-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R2-SRR3337501-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_16C_R2-SRR3337501-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R3-SRR3337502-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_16C_R3-SRR3337502-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R1-SRR3337503-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_36C_R1-SRR3337503-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R2-SRR3337504-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_36C_R2-SRR3337504-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R3-SRR3337505-TopHat-2.0.8/accepted_hits.bam SAMstats-smic_36C_R3-SRR3337505-TopHat-2.0.8 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R2-SRR3337493-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_nn_R2-SRR3337493-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R3-SRR3337494-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_nn_R3-SRR3337494-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R1-SRR3337495-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_DS_R1-SRR3337495-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R2-SRR3337496-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_DS_R2-SRR3337496-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_DS_R3-SRR3337497-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_DS_R3-SRR3337497-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_nn_R1-SRR3337498-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_nn_R1-SRR3337498-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R1-SRR3337500-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_16C_R1-SRR3337500-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R2-SRR3337501-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_16C_R2-SRR3337501-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_16C_R3-SRR3337502-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_16C_R3-SRR3337502-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R1-SRR3337503-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_36C_R1-SRR3337503-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R2-SRR3337504-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_36C_R2-SRR3337504-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py smic_36C_R3-SRR3337505-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-smic_36C_R3-SRR3337505-STAR-2.5.3a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.scaffold.final.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired &