cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.biaurelia.bwa.bam SAMstats-Sample_16I-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.biaurelia.bwa.bam SAMstats-Sample_C026-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.biaurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.biaurelia.bwa.bam SAMstats-Sample_M08-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.biaurelia.bwa.bam SAMstats-Sample_M13-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.biaurelia.bwa.bam SAMstats-Sample_M15-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.biaurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.biaurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.biaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.caudatum.bwa.bam SAMstats-Sample_16I-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.caudatum.bwa.bam SAMstats-Sample_C026-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.caudatum.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.caudatum.bwa.bam SAMstats-Sample_M08-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.caudatum.bwa.bam SAMstats-Sample_M13-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.caudatum.bwa.bam SAMstats-Sample_M15-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.caudatum.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.caudatum.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.caudatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_16I-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_C026-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_M08-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_M13-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_M15-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.multimicronucleatum.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.multimicronucleatum.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/multimicronucleatum_MO3c4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.octaurelia.bwa.bam SAMstats-Sample_16I-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.octaurelia.bwa.bam SAMstats-Sample_C026-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.octaurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.octaurelia.bwa.bam SAMstats-Sample_M08-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.octaurelia.bwa.bam SAMstats-Sample_M13-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.octaurelia.bwa.bam SAMstats-Sample_M15-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.octaurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.octaurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.octaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/Octaurelia_K8_CA1.scf.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_16I-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_C026-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_M08-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_M13-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_M15-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.pentaurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.pentaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/pentaurelia_87E+87O_SOAPassembly_draft.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.primaurelia.bwa.bam SAMstats-Sample_16I-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.primaurelia.bwa.bam SAMstats-Sample_C026-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.primaurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.primaurelia.bwa.bam SAMstats-Sample_M08-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.primaurelia.bwa.bam SAMstats-Sample_M13-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.primaurelia.bwa.bam SAMstats-Sample_M15-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.primaurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.primaurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.primaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_16I-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_C026-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_M08-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_M13-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_M15-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.sexaurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.sexaurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_16I-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_16I-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_C026-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Canal-1I-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_Canal-1I-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M08-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_M08-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_M13-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M15-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_M15-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_Peniche3I-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-reads.end1.tetraurelia.bwa.bam SAMstats-Sample_TRB101-4-reads.end1.tetraurelia.bwa -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &