cd /data/results/reference/bacteria/PseudomonasAeruginosa
/data/results/reference/bacteria/PseudomonasAeruginosa/build-bowtie2-indices.sh
IonXpress_003	YAbR21-OD3-B133-3	959,643,827	879,089,302	8,687,847	110 bp		UBAM BAM BAI
IonXpress_005	YAbR24-OD3-C3719-3	456,214,990	422,243,062	5,292,837	86 bp		UBAM BAM BAI

/data/images/proton2/run347/pip-pseu-aeru.sh
IonXpress_003	YAbR21-OD3-B133-3
8086125 reads; of these:
  8086125 (100.00%) were unpaired; of these:
    217419 (2.69%) aligned 0 times
    1812687 (22.42%) aligned exactly 1 time
    6056019 (74.89%) aligned >1 times
97.31% overall alignment rate

IonXpress_005	YAbR24-OD3-C3719-3
5050514 reads; of these:
  5050514 (100.00%) were unpaired; of these:
    2129053 (42.16%) aligned 0 times
    2117581 (41.93%) aligned exactly 1 time
    803880 (15.92%) aligned >1 times
57.84% overall alignment rate


cd /data/images/proton2/run347/tophat_005
samtools sort sort_uniq.bam sort_uniq.srt
samtools index sort_uniq.srt.bam 

/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie sort_uniq.srt.bam -p 8 -o C3719.gtf-e -B -G GCF_000152525.1_ASM15252v1_genomic.gff
/data/results/tools/rnaseq/stringtie/gffcompare-0.10.1.Linux_x86_64/gffcompare -r GCF_000152525.1_ASM15252v1_genomic.gff -o compare C3719.gtf

/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie sort_uniq.srt.bam -p 8 -o B136-33.gtf-B -G GCF_000359505.1_ASM35950v1_genomic.gff 
/data/results/tools/rnaseq/stringtie/gffcompare-0.10.1.Linux_x86_64/gffcompare -r GCF_000359505.1_ASM35950v1_genomic.gff -o compare B136-33.gtf 


#@using the PA14 as a popular reference genome 
reczko@max:/data/images/proton2/run347$ ./pip-pseu-aeru2.sh  &> pip-pseu-aeru2.log &

awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk C3719/GCF_000152525.1_ASM15252v1_genomic.gff 
awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk 
reczko@max:/data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa$ mv rRNA.gff C3719/GCF_000152525.1_ASM15252v1_genomic_rRNA.gff 
mv rRNA.gff C3719/GCF_000152525.1_ASM15252v1_genomic_rRNA.gff 
#/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -O --fraction -M -s 1 -J -f -g gene_name -t exon -T 4 -a   GCF_000152525.1_ASM15252v1_genomic.gff -o exon.cnt sort_uniq.srt.bam

/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -O --fraction -M -s 1 -J -f -g gene_name -t gene -T 4 -a   GCF_000152525.1_ASM15252v1_genomic.gff -o gene.cnt sort_uniq.srt.bam

/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -O --fraction -M -s 1 -J -f -g gene_name -t rRNA -T 4 -a   GCF_000152525.1_ASM15252v1_genomic_rRNA.gff -o rRNA.cnt sort_uniq.srt.bam
awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk gene.cnt
Sample	Total_mapped_reads
sort_uniq.srt.bam	2739311
awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk rRNA.cnt
Sample	Total_mapped_reads
sort_uniq.srt.bam	371275

reczko@max:/data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa$ awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk B136-33/GCF_000359505.1_ASM35950v1_genomic.gff 
awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk B136-33/GCF_000359505.1_ASM35950v1_genomic.gff 
reczko@max:/data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa$ mv rRNA.gff B136-33/GCF_000359505.1_ASM35950v1_genomic_rRNA.gff 

cd /data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa/B136-33
/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -O --fraction -M -s 1 -J -f -g gene_name -t gene -T 4 -a GCF_000359505.1_ASM35950v1_genomic.gff  -o gene.cnt sort_uniq.srt.bam
awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk gene.cnt
Sample	Total_mapped_reads
sort_uniq.srt.bam	7908761

awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk rRNA.cnt

Sample	Total_mapped_reads
sort_uniq.srt.bam	5946347


/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -O --fraction -M -s 1 -J -f -g gene_name -t rRNA -T 4 -a   GCF_000359505.1_ASM35950v1_genomic_rRNA.gff -o rRNA.cnt sort_uniq.srt.bam

reczko@max:/data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa$ awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk UCBPP-PA14/GCF_000014625.1_ASM1462v1_genomic.gff 
awk -f /data/results/reference/bacteria/PseudomonasAeruginosa/gff2rRNA.awk UCBPP-PA14/GCF_000014625.1_ASM1462v1_genomic.gff 
reczko@max:/data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa$ mv rRNA.gff UCBPP-PA14/GCF_000014625.1_ASM1462v1_genomic_rRNA.gff 
mv rRNA.gff UCBPP-PA14/GCF_000014625.1_ASM1462v1_genomic_rRNA.gff 

awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk YAbR24-OD3-C3719-3.gene.cnt
Sample	Total_mapped_reads
YAbR24-OD3-C3719-3.bam	4618578
awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk YAbR24-OD3-C3719-3.rRNA.cnt
Sample	Total_mapped_reads
YAbR24-OD3-C3719-3.bam	1980868
4777820 reads; of these:
  4777820 (100.00%) were unpaired; of these:
    292570 (6.12%) aligned 0 times
    2012491 (42.12%) aligned exactly 1 time
    2472759 (51.75%) aligned >1 times
93.88% overall alignment rate


awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk YAbR21-OD3-B133-3.gene.cnt
Sample	Total_mapped_reads
YAbR21-OD3-B133-3.bam	7839425
awk -f /data/images/proton2/run341/rpkm/getTotalReads.awk YAbR21-OD3-B133-3.rRNA.cnt
Sample	Total_mapped_reads
YAbR21-OD3-B133-3.bam	5958688
8161752 reads; of these:
  8161752 (100.00%) were unpaired; of these:
    317754 (3.89%) aligned 0 times
    1774200 (21.74%) aligned exactly 1 time
    6069798 (74.37%) aligned >1 times
96.11% overall alignment rate

#@ annotaion-species figure with
cd /data/images/proton2/run347/wwwDrApidianakis/PseudomonasAeruginosa/UCBPP-PA14/

/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/gffread GCF_000014625.1_ASM1462v1_genomic.gff -T -o UCBPP-PA14.gtf
samtools sort YAbR21-OD3-B133-3.bam  YAbR21-OD3-B133-3.sorted
samtools sort YAbR24-OD3-C3719-3.bam  YAbR24-OD3-C3719-3.sorted
cd /data/results/tools/qc/qualimap/qualimap_v2.2.1
qualimap