mkdir -p rna_s1221_S42/rna_s1221_S42.md/


cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > rna_s1221_S42/rna_s1221_S42.md/full_bed.bed


seqtool depth -bam rna_s1221_S42.md.bam -bed rna_s1221_S42/rna_s1221_S42.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz
saturation_plot       -bams rna_s1221_S42.md.bam       -region chr20       -output rna_s1221_S42/rna_s1221_S42.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/saturation_qc.tsv 
fragment_size       -bams rna_s1221_S42.md.bam       -region chr20       -output_prefix rna_s1221_S42/rna_s1221_S42.md/fragsize       -threads 1 
samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f ref_genome.fa   -l dbsnp_hg38_contam_sites.bed   rna_s1221_S42.md.bam > rna_s1221_S42.md.mpileup && contamination -input rna_s1221_S42.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > rna_s1221_S42/rna_s1221_S42.md/contamination.tsv 








tabix -s 1 -b 2 -e 2 rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz


seqtool depth_hist     -nbins 500     rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz     > rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth_hist.tsv


cat rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title rna_s1221_S42.md         -output rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.png




seqtool read_qc    -bed Twist_rna_exome_AND_fusion_hg38.bed     -n_threads 1     -bam_threads 2     rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool reads_per_target     -bed Twist_rna_exome_AND_fusion_hg38.bed     -threads 1     -bam_threads 2     rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
seqtool depth_stats  -bed Twist_rna_exome_AND_fusion_hg38.bed  rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz> rna_s1221_S42/rna_s1221_S42.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
seqtool gc_bias  -reference ref_genome.fa  -bed Twist_rna_exome_AND_fusion_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  rna_s1221_S42.md.bam  > rna_s1221_S42/rna_s1221_S42.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv 




cat rna_s1221_S42/rna_s1221_S42.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "rna_s1221_S42.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "rna_s1221_S42/rna_s1221_S42.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






echo `date` > rna_s1221_S42/rna_s1221_S42.md/qc_complete.txt