cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_1038-reads.end1.biaurelia.unique.bam SAMstats-Sample_1038-reads.end1.biaurelia -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_116-reads.end1.biaurelia.unique.bam SAMstats-Sample_116-reads.end1.biaurelia -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_126-reads.end1.biaurelia.unique.bam SAMstats-Sample_126-reads.end1.biaurelia -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_127-reads.end1.biaurelia.unique.bam SAMstats-Sample_127-reads.end1.biaurelia -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_128-reads.end1.biaurelia.unique.bam SAMstats-Sample_128-reads.end1.biaurelia -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_129-reads.end1.biaurelia.unique.bam SAMstats-Sample_129-reads.end1.biaurelia -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_130-reads.end1.biaurelia.unique.bam SAMstats-Sample_130-reads.end1.biaurelia -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_131-reads.end1.biaurelia.unique.bam SAMstats-Sample_131-reads.end1.biaurelia -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_132-reads.end1.biaurelia.unique.bam SAMstats-Sample_132-reads.end1.biaurelia -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_133-reads.end1.biaurelia.unique.bam SAMstats-Sample_133-reads.end1.biaurelia -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_134-reads.end1.biaurelia.unique.bam SAMstats-Sample_134-reads.end1.biaurelia -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_137-reads.end1.biaurelia.unique.bam SAMstats-Sample_137-reads.end1.biaurelia -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_169-reads.end1.biaurelia.unique.bam SAMstats-Sample_169-reads.end1.biaurelia -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.biaurelia.unique.bam SAMstats-Sample_16I-reads.end1.biaurelia -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_256-UB2-reads.end1.biaurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.biaurelia -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_258-UB4-reads.end1.biaurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.biaurelia -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_265-reads.end1.biaurelia.unique.bam SAMstats-Sample_265-reads.end1.biaurelia -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_291-reads.end1.biaurelia.unique.bam SAMstats-Sample_291-reads.end1.biaurelia -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_298-reads.end1.biaurelia.unique.bam SAMstats-Sample_298-reads.end1.biaurelia -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_31-reads.end1.biaurelia.unique.bam SAMstats-Sample_31-reads.end1.biaurelia -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_379-reads.end1.biaurelia.unique.bam SAMstats-Sample_379-reads.end1.biaurelia -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_44-reads.end1.biaurelia.unique.bam SAMstats-Sample_44-reads.end1.biaurelia -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_45-reads.end1.biaurelia.unique.bam SAMstats-Sample_45-reads.end1.biaurelia -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_47-reads.end1.biaurelia.unique.bam SAMstats-Sample_47-reads.end1.biaurelia -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_51-reads.end1.biaurelia.unique.bam SAMstats-Sample_51-reads.end1.biaurelia -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_562alpha-reads.end1.biaurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.biaurelia -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_76-reads.end1.biaurelia.unique.bam SAMstats-Sample_76-reads.end1.biaurelia -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_7K-reads.end1.biaurelia.unique.bam SAMstats-Sample_7K-reads.end1.biaurelia -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_98-reads.end1.biaurelia.unique.bam SAMstats-Sample_98-reads.end1.biaurelia -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_99-reads.end1.biaurelia.unique.bam SAMstats-Sample_99-reads.end1.biaurelia -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_A-reads.end1.biaurelia.unique.bam SAMstats-Sample_A-reads.end1.biaurelia -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_A30-reads.end1.biaurelia.unique.bam SAMstats-Sample_A30-reads.end1.biaurelia -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_B-reads.end1.biaurelia.unique.bam SAMstats-Sample_B-reads.end1.biaurelia -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_C023-reads.end1.biaurelia.unique.bam SAMstats-Sample_C023-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.biaurelia -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_C033-reads.end1.biaurelia.unique.bam SAMstats-Sample_C033-reads.end1.biaurelia -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_C065-reads.end1.biaurelia.unique.bam SAMstats-Sample_C065-reads.end1.biaurelia -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_C083-reads.end1.biaurelia.unique.bam SAMstats-Sample_C083-reads.end1.biaurelia -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_C104-reads.end1.biaurelia.unique.bam SAMstats-Sample_C104-reads.end1.biaurelia -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_C119-reads.end1.biaurelia.unique.bam SAMstats-Sample_C119-reads.end1.biaurelia -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_C131-reads.end1.biaurelia.unique.bam SAMstats-Sample_C131-reads.end1.biaurelia -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_C147-reads.end1.biaurelia.unique.bam SAMstats-Sample_C147-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.biaurelia -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_Indo1-7I-reads.end1.biaurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.biaurelia -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_M02-reads.end1.biaurelia.unique.bam SAMstats-Sample_M02-reads.end1.biaurelia -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_M03-reads.end1.biaurelia.unique.bam SAMstats-Sample_M03-reads.end1.biaurelia -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_M04-reads.end1.biaurelia.unique.bam SAMstats-Sample_M04-reads.end1.biaurelia -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_M05-reads.end1.biaurelia.unique.bam SAMstats-Sample_M05-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.biaurelia -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_M09-reads.end1.biaurelia.unique.bam SAMstats-Sample_M09-reads.end1.biaurelia -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_M12-reads.end1.biaurelia.unique.bam SAMstats-Sample_M12-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.biaurelia -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_Moz13BIII-reads.end1.biaurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.biaurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.biaurelia -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_USBL-36I1-reads.end1.biaurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.biaurelia -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_1038-reads.end1.caudatum.unique.bam SAMstats-Sample_1038-reads.end1.caudatum -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_116-reads.end1.caudatum.unique.bam SAMstats-Sample_116-reads.end1.caudatum -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_126-reads.end1.caudatum.unique.bam SAMstats-Sample_126-reads.end1.caudatum -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_127-reads.end1.caudatum.unique.bam SAMstats-Sample_127-reads.end1.caudatum -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_128-reads.end1.caudatum.unique.bam SAMstats-Sample_128-reads.end1.caudatum -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_129-reads.end1.caudatum.unique.bam SAMstats-Sample_129-reads.end1.caudatum -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_130-reads.end1.caudatum.unique.bam SAMstats-Sample_130-reads.end1.caudatum -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_131-reads.end1.caudatum.unique.bam SAMstats-Sample_131-reads.end1.caudatum -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_132-reads.end1.caudatum.unique.bam SAMstats-Sample_132-reads.end1.caudatum -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_133-reads.end1.caudatum.unique.bam SAMstats-Sample_133-reads.end1.caudatum -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_134-reads.end1.caudatum.unique.bam SAMstats-Sample_134-reads.end1.caudatum -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_137-reads.end1.caudatum.unique.bam SAMstats-Sample_137-reads.end1.caudatum -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_169-reads.end1.caudatum.unique.bam SAMstats-Sample_169-reads.end1.caudatum -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.caudatum.unique.bam SAMstats-Sample_16I-reads.end1.caudatum -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_256-UB2-reads.end1.caudatum.unique.bam SAMstats-Sample_256-UB2-reads.end1.caudatum -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_258-UB4-reads.end1.caudatum.unique.bam SAMstats-Sample_258-UB4-reads.end1.caudatum -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_265-reads.end1.caudatum.unique.bam SAMstats-Sample_265-reads.end1.caudatum -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_291-reads.end1.caudatum.unique.bam SAMstats-Sample_291-reads.end1.caudatum -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_298-reads.end1.caudatum.unique.bam SAMstats-Sample_298-reads.end1.caudatum -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_31-reads.end1.caudatum.unique.bam SAMstats-Sample_31-reads.end1.caudatum -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_379-reads.end1.caudatum.unique.bam SAMstats-Sample_379-reads.end1.caudatum -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_44-reads.end1.caudatum.unique.bam SAMstats-Sample_44-reads.end1.caudatum -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_45-reads.end1.caudatum.unique.bam SAMstats-Sample_45-reads.end1.caudatum -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_47-reads.end1.caudatum.unique.bam SAMstats-Sample_47-reads.end1.caudatum -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_51-reads.end1.caudatum.unique.bam SAMstats-Sample_51-reads.end1.caudatum -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_562alpha-reads.end1.caudatum.unique.bam SAMstats-Sample_562alpha-reads.end1.caudatum -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_76-reads.end1.caudatum.unique.bam SAMstats-Sample_76-reads.end1.caudatum -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_7K-reads.end1.caudatum.unique.bam SAMstats-Sample_7K-reads.end1.caudatum -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_98-reads.end1.caudatum.unique.bam SAMstats-Sample_98-reads.end1.caudatum -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_99-reads.end1.caudatum.unique.bam SAMstats-Sample_99-reads.end1.caudatum -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_A-reads.end1.caudatum.unique.bam SAMstats-Sample_A-reads.end1.caudatum -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_A30-reads.end1.caudatum.unique.bam SAMstats-Sample_A30-reads.end1.caudatum -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_B-reads.end1.caudatum.unique.bam SAMstats-Sample_B-reads.end1.caudatum -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_C023-reads.end1.caudatum.unique.bam SAMstats-Sample_C023-reads.end1.caudatum -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.unique.bam SAMstats-Sample_C026-reads.end1.caudatum -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_C033-reads.end1.caudatum.unique.bam SAMstats-Sample_C033-reads.end1.caudatum -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_C065-reads.end1.caudatum.unique.bam SAMstats-Sample_C065-reads.end1.caudatum -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_C083-reads.end1.caudatum.unique.bam SAMstats-Sample_C083-reads.end1.caudatum -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_C104-reads.end1.caudatum.unique.bam SAMstats-Sample_C104-reads.end1.caudatum -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_C119-reads.end1.caudatum.unique.bam SAMstats-Sample_C119-reads.end1.caudatum -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_C131-reads.end1.caudatum.unique.bam SAMstats-Sample_C131-reads.end1.caudatum -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_C147-reads.end1.caudatum.unique.bam SAMstats-Sample_C147-reads.end1.caudatum -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.caudatum -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_Indo1-7I-reads.end1.caudatum.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.caudatum -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_M02-reads.end1.caudatum.unique.bam SAMstats-Sample_M02-reads.end1.caudatum -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_M03-reads.end1.caudatum.unique.bam SAMstats-Sample_M03-reads.end1.caudatum -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_M04-reads.end1.caudatum.unique.bam SAMstats-Sample_M04-reads.end1.caudatum -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_M05-reads.end1.caudatum.unique.bam SAMstats-Sample_M05-reads.end1.caudatum -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.unique.bam SAMstats-Sample_M08-reads.end1.caudatum -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_M09-reads.end1.caudatum.unique.bam SAMstats-Sample_M09-reads.end1.caudatum -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_M12-reads.end1.caudatum.unique.bam SAMstats-Sample_M12-reads.end1.caudatum -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.unique.bam SAMstats-Sample_M13-reads.end1.caudatum -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.unique.bam SAMstats-Sample_M15-reads.end1.caudatum -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_Moz13BIII-reads.end1.caudatum.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.caudatum -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.caudatum -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.caudatum -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_USBL-36I1-reads.end1.caudatum.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.caudatum -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_1038-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_1038-reads.end1.multimicronucleatum -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_116-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_116-reads.end1.multimicronucleatum -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_126-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_126-reads.end1.multimicronucleatum -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_127-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_127-reads.end1.multimicronucleatum -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_128-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_128-reads.end1.multimicronucleatum -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_129-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_129-reads.end1.multimicronucleatum -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_130-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_130-reads.end1.multimicronucleatum -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_131-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_131-reads.end1.multimicronucleatum -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_132-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_132-reads.end1.multimicronucleatum -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_133-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_133-reads.end1.multimicronucleatum -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_134-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_134-reads.end1.multimicronucleatum -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_137-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_137-reads.end1.multimicronucleatum -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_169-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_169-reads.end1.multimicronucleatum -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.multimicronucleatum.unique.bam SAMstats-Sample_16I-reads.end1.multimicronucleatum -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_256-UB2-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_256-UB2-reads.end1.multimicronucleatum -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_258-UB4-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_258-UB4-reads.end1.multimicronucleatum -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_265-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_265-reads.end1.multimicronucleatum -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_291-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_291-reads.end1.multimicronucleatum -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_298-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_298-reads.end1.multimicronucleatum -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_31-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_31-reads.end1.multimicronucleatum -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_379-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_379-reads.end1.multimicronucleatum -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_44-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_44-reads.end1.multimicronucleatum -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_45-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_45-reads.end1.multimicronucleatum -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_47-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_47-reads.end1.multimicronucleatum -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_51-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_51-reads.end1.multimicronucleatum -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_562alpha-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_562alpha-reads.end1.multimicronucleatum -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_76-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_76-reads.end1.multimicronucleatum -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_7K-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_7K-reads.end1.multimicronucleatum -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_98-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_98-reads.end1.multimicronucleatum -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_99-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_99-reads.end1.multimicronucleatum -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_A-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_A-reads.end1.multimicronucleatum -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_A30-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_A30-reads.end1.multimicronucleatum -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_B-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_B-reads.end1.multimicronucleatum -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_C023-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C023-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_C026-reads.end1.multimicronucleatum -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_C033-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C033-reads.end1.multimicronucleatum -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_C065-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C065-reads.end1.multimicronucleatum -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_C083-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C083-reads.end1.multimicronucleatum -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_C104-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C104-reads.end1.multimicronucleatum -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_C119-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C119-reads.end1.multimicronucleatum -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_C131-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C131-reads.end1.multimicronucleatum -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_C147-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_C147-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.multimicronucleatum -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_Indo1-7I-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.multimicronucleatum -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_M02-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M02-reads.end1.multimicronucleatum -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_M03-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M03-reads.end1.multimicronucleatum -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_M04-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M04-reads.end1.multimicronucleatum -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_M05-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M05-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_M08-reads.end1.multimicronucleatum -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_M09-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M09-reads.end1.multimicronucleatum -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_M12-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_M12-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_M13-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_M15-reads.end1.multimicronucleatum -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_Moz13BIII-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.multimicronucleatum -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.multimicronucleatum -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_USBL-36I1-reads.end1.multimicronucleatum.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.multimicronucleatum -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_1038-reads.end1.octaurelia.unique.bam SAMstats-Sample_1038-reads.end1.octaurelia -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_116-reads.end1.octaurelia.unique.bam SAMstats-Sample_116-reads.end1.octaurelia -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_126-reads.end1.octaurelia.unique.bam SAMstats-Sample_126-reads.end1.octaurelia -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_127-reads.end1.octaurelia.unique.bam SAMstats-Sample_127-reads.end1.octaurelia -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_128-reads.end1.octaurelia.unique.bam SAMstats-Sample_128-reads.end1.octaurelia -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_129-reads.end1.octaurelia.unique.bam SAMstats-Sample_129-reads.end1.octaurelia -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_130-reads.end1.octaurelia.unique.bam SAMstats-Sample_130-reads.end1.octaurelia -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_131-reads.end1.octaurelia.unique.bam SAMstats-Sample_131-reads.end1.octaurelia -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_132-reads.end1.octaurelia.unique.bam SAMstats-Sample_132-reads.end1.octaurelia -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_133-reads.end1.octaurelia.unique.bam SAMstats-Sample_133-reads.end1.octaurelia -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_134-reads.end1.octaurelia.unique.bam SAMstats-Sample_134-reads.end1.octaurelia -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_137-reads.end1.octaurelia.unique.bam SAMstats-Sample_137-reads.end1.octaurelia -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_169-reads.end1.octaurelia.unique.bam SAMstats-Sample_169-reads.end1.octaurelia -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.octaurelia.unique.bam SAMstats-Sample_16I-reads.end1.octaurelia -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_256-UB2-reads.end1.octaurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.octaurelia -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_258-UB4-reads.end1.octaurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.octaurelia -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_265-reads.end1.octaurelia.unique.bam SAMstats-Sample_265-reads.end1.octaurelia -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_291-reads.end1.octaurelia.unique.bam SAMstats-Sample_291-reads.end1.octaurelia -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_298-reads.end1.octaurelia.unique.bam SAMstats-Sample_298-reads.end1.octaurelia -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_31-reads.end1.octaurelia.unique.bam SAMstats-Sample_31-reads.end1.octaurelia -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_379-reads.end1.octaurelia.unique.bam SAMstats-Sample_379-reads.end1.octaurelia -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_44-reads.end1.octaurelia.unique.bam SAMstats-Sample_44-reads.end1.octaurelia -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_45-reads.end1.octaurelia.unique.bam SAMstats-Sample_45-reads.end1.octaurelia -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_47-reads.end1.octaurelia.unique.bam SAMstats-Sample_47-reads.end1.octaurelia -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_51-reads.end1.octaurelia.unique.bam SAMstats-Sample_51-reads.end1.octaurelia -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_562alpha-reads.end1.octaurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.octaurelia -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_76-reads.end1.octaurelia.unique.bam SAMstats-Sample_76-reads.end1.octaurelia -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_7K-reads.end1.octaurelia.unique.bam SAMstats-Sample_7K-reads.end1.octaurelia -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_98-reads.end1.octaurelia.unique.bam SAMstats-Sample_98-reads.end1.octaurelia -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_99-reads.end1.octaurelia.unique.bam SAMstats-Sample_99-reads.end1.octaurelia -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_A-reads.end1.octaurelia.unique.bam SAMstats-Sample_A-reads.end1.octaurelia -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_A30-reads.end1.octaurelia.unique.bam SAMstats-Sample_A30-reads.end1.octaurelia -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_B-reads.end1.octaurelia.unique.bam SAMstats-Sample_B-reads.end1.octaurelia -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_C023-reads.end1.octaurelia.unique.bam SAMstats-Sample_C023-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.octaurelia -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_C033-reads.end1.octaurelia.unique.bam SAMstats-Sample_C033-reads.end1.octaurelia -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_C065-reads.end1.octaurelia.unique.bam SAMstats-Sample_C065-reads.end1.octaurelia -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_C083-reads.end1.octaurelia.unique.bam SAMstats-Sample_C083-reads.end1.octaurelia -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_C104-reads.end1.octaurelia.unique.bam SAMstats-Sample_C104-reads.end1.octaurelia -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_C119-reads.end1.octaurelia.unique.bam SAMstats-Sample_C119-reads.end1.octaurelia -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_C131-reads.end1.octaurelia.unique.bam SAMstats-Sample_C131-reads.end1.octaurelia -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_C147-reads.end1.octaurelia.unique.bam SAMstats-Sample_C147-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.octaurelia -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_Indo1-7I-reads.end1.octaurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.octaurelia -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_M02-reads.end1.octaurelia.unique.bam SAMstats-Sample_M02-reads.end1.octaurelia -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_M03-reads.end1.octaurelia.unique.bam SAMstats-Sample_M03-reads.end1.octaurelia -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_M04-reads.end1.octaurelia.unique.bam SAMstats-Sample_M04-reads.end1.octaurelia -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_M05-reads.end1.octaurelia.unique.bam SAMstats-Sample_M05-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.octaurelia -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_M09-reads.end1.octaurelia.unique.bam SAMstats-Sample_M09-reads.end1.octaurelia -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_M12-reads.end1.octaurelia.unique.bam SAMstats-Sample_M12-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.octaurelia -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_Moz13BIII-reads.end1.octaurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.octaurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.octaurelia -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_USBL-36I1-reads.end1.octaurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.octaurelia -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_1038-reads.end1.pentaurelia.unique.bam SAMstats-Sample_1038-reads.end1.pentaurelia -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_116-reads.end1.pentaurelia.unique.bam SAMstats-Sample_116-reads.end1.pentaurelia -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_126-reads.end1.pentaurelia.unique.bam SAMstats-Sample_126-reads.end1.pentaurelia -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_127-reads.end1.pentaurelia.unique.bam SAMstats-Sample_127-reads.end1.pentaurelia -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_128-reads.end1.pentaurelia.unique.bam SAMstats-Sample_128-reads.end1.pentaurelia -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_129-reads.end1.pentaurelia.unique.bam SAMstats-Sample_129-reads.end1.pentaurelia -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_130-reads.end1.pentaurelia.unique.bam SAMstats-Sample_130-reads.end1.pentaurelia -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_131-reads.end1.pentaurelia.unique.bam SAMstats-Sample_131-reads.end1.pentaurelia -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_132-reads.end1.pentaurelia.unique.bam SAMstats-Sample_132-reads.end1.pentaurelia -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_133-reads.end1.pentaurelia.unique.bam SAMstats-Sample_133-reads.end1.pentaurelia -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_134-reads.end1.pentaurelia.unique.bam SAMstats-Sample_134-reads.end1.pentaurelia -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_137-reads.end1.pentaurelia.unique.bam SAMstats-Sample_137-reads.end1.pentaurelia -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_169-reads.end1.pentaurelia.unique.bam SAMstats-Sample_169-reads.end1.pentaurelia -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.pentaurelia.unique.bam SAMstats-Sample_16I-reads.end1.pentaurelia -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_256-UB2-reads.end1.pentaurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.pentaurelia -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_258-UB4-reads.end1.pentaurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.pentaurelia -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_265-reads.end1.pentaurelia.unique.bam SAMstats-Sample_265-reads.end1.pentaurelia -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_291-reads.end1.pentaurelia.unique.bam SAMstats-Sample_291-reads.end1.pentaurelia -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_298-reads.end1.pentaurelia.unique.bam SAMstats-Sample_298-reads.end1.pentaurelia -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_31-reads.end1.pentaurelia.unique.bam SAMstats-Sample_31-reads.end1.pentaurelia -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_379-reads.end1.pentaurelia.unique.bam SAMstats-Sample_379-reads.end1.pentaurelia -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_44-reads.end1.pentaurelia.unique.bam SAMstats-Sample_44-reads.end1.pentaurelia -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_45-reads.end1.pentaurelia.unique.bam SAMstats-Sample_45-reads.end1.pentaurelia -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_47-reads.end1.pentaurelia.unique.bam SAMstats-Sample_47-reads.end1.pentaurelia -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_51-reads.end1.pentaurelia.unique.bam SAMstats-Sample_51-reads.end1.pentaurelia -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_562alpha-reads.end1.pentaurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.pentaurelia -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_76-reads.end1.pentaurelia.unique.bam SAMstats-Sample_76-reads.end1.pentaurelia -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_7K-reads.end1.pentaurelia.unique.bam SAMstats-Sample_7K-reads.end1.pentaurelia -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_98-reads.end1.pentaurelia.unique.bam SAMstats-Sample_98-reads.end1.pentaurelia -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_99-reads.end1.pentaurelia.unique.bam SAMstats-Sample_99-reads.end1.pentaurelia -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_A-reads.end1.pentaurelia.unique.bam SAMstats-Sample_A-reads.end1.pentaurelia -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_A30-reads.end1.pentaurelia.unique.bam SAMstats-Sample_A30-reads.end1.pentaurelia -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_B-reads.end1.pentaurelia.unique.bam SAMstats-Sample_B-reads.end1.pentaurelia -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_C023-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C023-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.pentaurelia -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_C033-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C033-reads.end1.pentaurelia -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_C065-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C065-reads.end1.pentaurelia -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_C083-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C083-reads.end1.pentaurelia -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_C104-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C104-reads.end1.pentaurelia -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_C119-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C119-reads.end1.pentaurelia -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_C131-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C131-reads.end1.pentaurelia -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_C147-reads.end1.pentaurelia.unique.bam SAMstats-Sample_C147-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.pentaurelia -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_Indo1-7I-reads.end1.pentaurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.pentaurelia -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_M02-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M02-reads.end1.pentaurelia -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_M03-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M03-reads.end1.pentaurelia -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_M04-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M04-reads.end1.pentaurelia -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_M05-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M05-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.pentaurelia -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_M09-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M09-reads.end1.pentaurelia -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_M12-reads.end1.pentaurelia.unique.bam SAMstats-Sample_M12-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.pentaurelia -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_Moz13BIII-reads.end1.pentaurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.pentaurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.pentaurelia -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_USBL-36I1-reads.end1.pentaurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.pentaurelia -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_1038-reads.end1.primaurelia.unique.bam SAMstats-Sample_1038-reads.end1.primaurelia -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_116-reads.end1.primaurelia.unique.bam SAMstats-Sample_116-reads.end1.primaurelia -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_126-reads.end1.primaurelia.unique.bam SAMstats-Sample_126-reads.end1.primaurelia -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_127-reads.end1.primaurelia.unique.bam SAMstats-Sample_127-reads.end1.primaurelia -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_128-reads.end1.primaurelia.unique.bam SAMstats-Sample_128-reads.end1.primaurelia -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_129-reads.end1.primaurelia.unique.bam SAMstats-Sample_129-reads.end1.primaurelia -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_130-reads.end1.primaurelia.unique.bam SAMstats-Sample_130-reads.end1.primaurelia -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_131-reads.end1.primaurelia.unique.bam SAMstats-Sample_131-reads.end1.primaurelia -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_132-reads.end1.primaurelia.unique.bam SAMstats-Sample_132-reads.end1.primaurelia -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_133-reads.end1.primaurelia.unique.bam SAMstats-Sample_133-reads.end1.primaurelia -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_134-reads.end1.primaurelia.unique.bam SAMstats-Sample_134-reads.end1.primaurelia -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_137-reads.end1.primaurelia.unique.bam SAMstats-Sample_137-reads.end1.primaurelia -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_169-reads.end1.primaurelia.unique.bam SAMstats-Sample_169-reads.end1.primaurelia -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.primaurelia.unique.bam SAMstats-Sample_16I-reads.end1.primaurelia -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_256-UB2-reads.end1.primaurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.primaurelia -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_258-UB4-reads.end1.primaurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.primaurelia -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_265-reads.end1.primaurelia.unique.bam SAMstats-Sample_265-reads.end1.primaurelia -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_291-reads.end1.primaurelia.unique.bam SAMstats-Sample_291-reads.end1.primaurelia -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_298-reads.end1.primaurelia.unique.bam SAMstats-Sample_298-reads.end1.primaurelia -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_31-reads.end1.primaurelia.unique.bam SAMstats-Sample_31-reads.end1.primaurelia -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_379-reads.end1.primaurelia.unique.bam SAMstats-Sample_379-reads.end1.primaurelia -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_44-reads.end1.primaurelia.unique.bam SAMstats-Sample_44-reads.end1.primaurelia -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_45-reads.end1.primaurelia.unique.bam SAMstats-Sample_45-reads.end1.primaurelia -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_47-reads.end1.primaurelia.unique.bam SAMstats-Sample_47-reads.end1.primaurelia -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_51-reads.end1.primaurelia.unique.bam SAMstats-Sample_51-reads.end1.primaurelia -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_562alpha-reads.end1.primaurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.primaurelia -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_76-reads.end1.primaurelia.unique.bam SAMstats-Sample_76-reads.end1.primaurelia -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_7K-reads.end1.primaurelia.unique.bam SAMstats-Sample_7K-reads.end1.primaurelia -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_98-reads.end1.primaurelia.unique.bam SAMstats-Sample_98-reads.end1.primaurelia -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_99-reads.end1.primaurelia.unique.bam SAMstats-Sample_99-reads.end1.primaurelia -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_A-reads.end1.primaurelia.unique.bam SAMstats-Sample_A-reads.end1.primaurelia -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_A30-reads.end1.primaurelia.unique.bam SAMstats-Sample_A30-reads.end1.primaurelia -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_B-reads.end1.primaurelia.unique.bam SAMstats-Sample_B-reads.end1.primaurelia -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_C023-reads.end1.primaurelia.unique.bam SAMstats-Sample_C023-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.primaurelia -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_C033-reads.end1.primaurelia.unique.bam SAMstats-Sample_C033-reads.end1.primaurelia -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_C065-reads.end1.primaurelia.unique.bam SAMstats-Sample_C065-reads.end1.primaurelia -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_C083-reads.end1.primaurelia.unique.bam SAMstats-Sample_C083-reads.end1.primaurelia -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_C104-reads.end1.primaurelia.unique.bam SAMstats-Sample_C104-reads.end1.primaurelia -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_C119-reads.end1.primaurelia.unique.bam SAMstats-Sample_C119-reads.end1.primaurelia -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_C131-reads.end1.primaurelia.unique.bam SAMstats-Sample_C131-reads.end1.primaurelia -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_C147-reads.end1.primaurelia.unique.bam SAMstats-Sample_C147-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.primaurelia -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_Indo1-7I-reads.end1.primaurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.primaurelia -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_M02-reads.end1.primaurelia.unique.bam SAMstats-Sample_M02-reads.end1.primaurelia -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_M03-reads.end1.primaurelia.unique.bam SAMstats-Sample_M03-reads.end1.primaurelia -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_M04-reads.end1.primaurelia.unique.bam SAMstats-Sample_M04-reads.end1.primaurelia -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_M05-reads.end1.primaurelia.unique.bam SAMstats-Sample_M05-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.primaurelia -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_M09-reads.end1.primaurelia.unique.bam SAMstats-Sample_M09-reads.end1.primaurelia -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_M12-reads.end1.primaurelia.unique.bam SAMstats-Sample_M12-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.primaurelia -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_Moz13BIII-reads.end1.primaurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.primaurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.primaurelia -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_USBL-36I1-reads.end1.primaurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.primaurelia -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_1038-reads.end1.sexaurelia.unique.bam SAMstats-Sample_1038-reads.end1.sexaurelia -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_116-reads.end1.sexaurelia.unique.bam SAMstats-Sample_116-reads.end1.sexaurelia -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_126-reads.end1.sexaurelia.unique.bam SAMstats-Sample_126-reads.end1.sexaurelia -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_127-reads.end1.sexaurelia.unique.bam SAMstats-Sample_127-reads.end1.sexaurelia -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_128-reads.end1.sexaurelia.unique.bam SAMstats-Sample_128-reads.end1.sexaurelia -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_129-reads.end1.sexaurelia.unique.bam SAMstats-Sample_129-reads.end1.sexaurelia -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_130-reads.end1.sexaurelia.unique.bam SAMstats-Sample_130-reads.end1.sexaurelia -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_131-reads.end1.sexaurelia.unique.bam SAMstats-Sample_131-reads.end1.sexaurelia -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_132-reads.end1.sexaurelia.unique.bam SAMstats-Sample_132-reads.end1.sexaurelia -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_133-reads.end1.sexaurelia.unique.bam SAMstats-Sample_133-reads.end1.sexaurelia -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_134-reads.end1.sexaurelia.unique.bam SAMstats-Sample_134-reads.end1.sexaurelia -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_137-reads.end1.sexaurelia.unique.bam SAMstats-Sample_137-reads.end1.sexaurelia -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_169-reads.end1.sexaurelia.unique.bam SAMstats-Sample_169-reads.end1.sexaurelia -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.sexaurelia.unique.bam SAMstats-Sample_16I-reads.end1.sexaurelia -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_256-UB2-reads.end1.sexaurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.sexaurelia -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_258-UB4-reads.end1.sexaurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.sexaurelia -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_265-reads.end1.sexaurelia.unique.bam SAMstats-Sample_265-reads.end1.sexaurelia -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_291-reads.end1.sexaurelia.unique.bam SAMstats-Sample_291-reads.end1.sexaurelia -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_298-reads.end1.sexaurelia.unique.bam SAMstats-Sample_298-reads.end1.sexaurelia -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_31-reads.end1.sexaurelia.unique.bam SAMstats-Sample_31-reads.end1.sexaurelia -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_379-reads.end1.sexaurelia.unique.bam SAMstats-Sample_379-reads.end1.sexaurelia -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_44-reads.end1.sexaurelia.unique.bam SAMstats-Sample_44-reads.end1.sexaurelia -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_45-reads.end1.sexaurelia.unique.bam SAMstats-Sample_45-reads.end1.sexaurelia -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_47-reads.end1.sexaurelia.unique.bam SAMstats-Sample_47-reads.end1.sexaurelia -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_51-reads.end1.sexaurelia.unique.bam SAMstats-Sample_51-reads.end1.sexaurelia -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_562alpha-reads.end1.sexaurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.sexaurelia -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_76-reads.end1.sexaurelia.unique.bam SAMstats-Sample_76-reads.end1.sexaurelia -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_7K-reads.end1.sexaurelia.unique.bam SAMstats-Sample_7K-reads.end1.sexaurelia -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_98-reads.end1.sexaurelia.unique.bam SAMstats-Sample_98-reads.end1.sexaurelia -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_99-reads.end1.sexaurelia.unique.bam SAMstats-Sample_99-reads.end1.sexaurelia -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_A-reads.end1.sexaurelia.unique.bam SAMstats-Sample_A-reads.end1.sexaurelia -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_A30-reads.end1.sexaurelia.unique.bam SAMstats-Sample_A30-reads.end1.sexaurelia -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_B-reads.end1.sexaurelia.unique.bam SAMstats-Sample_B-reads.end1.sexaurelia -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_C023-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C023-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.sexaurelia -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_C033-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C033-reads.end1.sexaurelia -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_C065-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C065-reads.end1.sexaurelia -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_C083-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C083-reads.end1.sexaurelia -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_C104-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C104-reads.end1.sexaurelia -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_C119-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C119-reads.end1.sexaurelia -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_C131-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C131-reads.end1.sexaurelia -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_C147-reads.end1.sexaurelia.unique.bam SAMstats-Sample_C147-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.sexaurelia -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_Indo1-7I-reads.end1.sexaurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.sexaurelia -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_M02-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M02-reads.end1.sexaurelia -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_M03-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M03-reads.end1.sexaurelia -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_M04-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M04-reads.end1.sexaurelia -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_M05-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M05-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.sexaurelia -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_M09-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M09-reads.end1.sexaurelia -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_M12-reads.end1.sexaurelia.unique.bam SAMstats-Sample_M12-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.sexaurelia -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_Moz13BIII-reads.end1.sexaurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.sexaurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.sexaurelia -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_USBL-36I1-reads.end1.sexaurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.sexaurelia -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_1038-reads.end1.tetraurelia.unique.bam SAMstats-Sample_1038-reads.end1.tetraurelia -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_116-reads.end1.tetraurelia.unique.bam SAMstats-Sample_116-reads.end1.tetraurelia -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_126-reads.end1.tetraurelia.unique.bam SAMstats-Sample_126-reads.end1.tetraurelia -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_127-reads.end1.tetraurelia.unique.bam SAMstats-Sample_127-reads.end1.tetraurelia -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_128-reads.end1.tetraurelia.unique.bam SAMstats-Sample_128-reads.end1.tetraurelia -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_129-reads.end1.tetraurelia.unique.bam SAMstats-Sample_129-reads.end1.tetraurelia -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_130-reads.end1.tetraurelia.unique.bam SAMstats-Sample_130-reads.end1.tetraurelia -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_131-reads.end1.tetraurelia.unique.bam SAMstats-Sample_131-reads.end1.tetraurelia -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_132-reads.end1.tetraurelia.unique.bam SAMstats-Sample_132-reads.end1.tetraurelia -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_133-reads.end1.tetraurelia.unique.bam SAMstats-Sample_133-reads.end1.tetraurelia -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_134-reads.end1.tetraurelia.unique.bam SAMstats-Sample_134-reads.end1.tetraurelia -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_137-reads.end1.tetraurelia.unique.bam SAMstats-Sample_137-reads.end1.tetraurelia -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_169-reads.end1.tetraurelia.unique.bam SAMstats-Sample_169-reads.end1.tetraurelia -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_16I-reads.end1.tetraurelia.unique.bam SAMstats-Sample_16I-reads.end1.tetraurelia -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_256-UB2-reads.end1.tetraurelia.unique.bam SAMstats-Sample_256-UB2-reads.end1.tetraurelia -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_258-UB4-reads.end1.tetraurelia.unique.bam SAMstats-Sample_258-UB4-reads.end1.tetraurelia -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_265-reads.end1.tetraurelia.unique.bam SAMstats-Sample_265-reads.end1.tetraurelia -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_291-reads.end1.tetraurelia.unique.bam SAMstats-Sample_291-reads.end1.tetraurelia -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_298-reads.end1.tetraurelia.unique.bam SAMstats-Sample_298-reads.end1.tetraurelia -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_31-reads.end1.tetraurelia.unique.bam SAMstats-Sample_31-reads.end1.tetraurelia -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_379-reads.end1.tetraurelia.unique.bam SAMstats-Sample_379-reads.end1.tetraurelia -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_44-reads.end1.tetraurelia.unique.bam SAMstats-Sample_44-reads.end1.tetraurelia -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_45-reads.end1.tetraurelia.unique.bam SAMstats-Sample_45-reads.end1.tetraurelia -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_47-reads.end1.tetraurelia.unique.bam SAMstats-Sample_47-reads.end1.tetraurelia -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_51-reads.end1.tetraurelia.unique.bam SAMstats-Sample_51-reads.end1.tetraurelia -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_562alpha-reads.end1.tetraurelia.unique.bam SAMstats-Sample_562alpha-reads.end1.tetraurelia -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_76-reads.end1.tetraurelia.unique.bam SAMstats-Sample_76-reads.end1.tetraurelia -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_7K-reads.end1.tetraurelia.unique.bam SAMstats-Sample_7K-reads.end1.tetraurelia -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_98-reads.end1.tetraurelia.unique.bam SAMstats-Sample_98-reads.end1.tetraurelia -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_99-reads.end1.tetraurelia.unique.bam SAMstats-Sample_99-reads.end1.tetraurelia -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_A-reads.end1.tetraurelia.unique.bam SAMstats-Sample_A-reads.end1.tetraurelia -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_A30-reads.end1.tetraurelia.unique.bam SAMstats-Sample_A30-reads.end1.tetraurelia -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_B-reads.end1.tetraurelia.unique.bam SAMstats-Sample_B-reads.end1.tetraurelia -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_C023-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C023-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_C026-reads.end1.tetraurelia -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_C033-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C033-reads.end1.tetraurelia -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_C065-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C065-reads.end1.tetraurelia -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_C083-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C083-reads.end1.tetraurelia -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_C104-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C104-reads.end1.tetraurelia -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_C119-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C119-reads.end1.tetraurelia -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_C131-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C131-reads.end1.tetraurelia -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_C147-reads.end1.tetraurelia.unique.bam SAMstats-Sample_C147-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_Canal-1I-reads.end1.tetraurelia -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_Indo1-7I-reads.end1.tetraurelia.unique.bam SAMstats-Sample_Indo1-7I-reads.end1.tetraurelia -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_M02-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M02-reads.end1.tetraurelia -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_M03-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M03-reads.end1.tetraurelia -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_M04-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M04-reads.end1.tetraurelia -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_M05-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M05-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_M08-reads.end1.tetraurelia -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_M09-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M09-reads.end1.tetraurelia -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_M12-reads.end1.tetraurelia.unique.bam SAMstats-Sample_M12-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_M13-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_M15-reads.end1.tetraurelia -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_Moz13BIII-reads.end1.tetraurelia.unique.bam SAMstats-Sample_Moz13BIII-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_Peniche3I-reads.end1.tetraurelia -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.unique.bam SAMstats-Sample_TRB101-4-reads.end1.tetraurelia -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_USBL-36I1-reads.end1.tetraurelia.unique.bam SAMstats-Sample_USBL-36I1-reads.end1.tetraurelia -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.chrom.sizes samtools &