cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/SAMstats.py Paramecium-caudatum-Hol_S14-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam SAMstats-Paramecium-caudatum-Hol_S14-2x100 -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/SAMstats.py Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam SAMstats-Paramecium-caudatum-no-Hol_S15-2x100 -bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-Hol_S14-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-Hol_S14-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-no-Hol_S15-2x100 -nomulti