cd pTrc8 ln -s /home/reczko/bak/doc/klpno/run362/pTrc8_Fasta_Sequence_02.dna #/data/results/tools/align/bowtie2-2.2.9/bowtie2-build pTrc8_Fasta_Sequence_02.dna pTrc8 /data/results/tools/align/hisat/hisat2-2.1.0/hisat2-build pTrc8_Fasta_Sequence_02.dna pTrc8 samtools faidx pTrc8_Fasta_Sequence_02.dna /data/results/tools/align/bowtie2-2.2.8/bowtie2-build pTrc8_Fasta_Sequence_02.dna pTrc8 /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc8-23600-25660.fa cd ~/bak/doc/klpno/run362/run362/klpno/pTrc502/ ln -s /home/reczko/bak/doc/klpno/run362/pTrc502_Fasta_Sequence_04.dna #/data/results/tools/align/bowtie2-2.2.9/bowtie2-build pTrc502_Fasta_Sequence_04.dna pTrc502 /data/results/tools/align/hisat/hisat2-2.1.0/hisat2-build pTrc502_Fasta_Sequence_04.dna pTrc502 /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc502-30300-41000.fa reczko@max:~/bak/doc/klpno/run362/run362/klpno/pTrc502$ samtools faidx pTrc502_Fasta_Sequence_04.dna cd ../WG5 /data/results/tools/align/hisat/hisat2-2.1.0/hisat2-build WG5.fasta WG5 /data/results/tools/align/bowtie2-2.2.8/bowtie2-build WG5.fasta WG5 /data/results/tools/align/bwa/bwa-0.7.16a/bwa index WG5.fasta reczko@max:/data/results/tools/align/longest-unique-seq$ g++ longest-unique-seq.cpp reczko@max:/data/results/tools/align/longest-unique-seq$ ./a.out Max sustring is : gaaggttttaaagaaggttttaaagaaggttttaaagaaggttttaagaaaggtg with length 55 /data/results/tools/align/cdhit/cdhit-master/cd-hit-est-2d -i pTrc8/pTrc8_Fasta_Sequence_02.dna -i2 pTrc502/pTrc502_Fasta_Sequence_04.dna -o 8vs502 -T 10 -G 0 /data/results/tools/align/mumer/MUMmer3.23/run-mummer3 pTrc8/pTrc8_Fasta_Sequence_02.dna pTrc502/pTrc502_Fasta_Sequence_04.dna 8vs502 /data/results/tools/align/mumer/MUMmer3.23/mummerplot 8vs502.out 8: 23600-25660 502:30300-41000 /data/results/tools/align/mumer/MUMmer3.23/mummerplot 8vs502.out --png cp out.png 8vs502.png /data/results/tools/align/mumer/MUMmer3.23/run-mummer3 WG5/WG5.fasta pTrc8/pTrc8_Fasta_Sequence_02.dna WG5vs8 /data/results/tools/align/mumer/MUMmer3.23/mummerplot WG5vs8.out --png cp out.png WG5vs8.png /data/results/tools/align/mumer/MUMmer3.23/run-mummer3 WG5/WG5.fasta pTrc502/pTrc502_Fasta_Sequence_04.dna WG5vs502 /data/results/tools/align/mumer/MUMmer3.23/mummerplot WG5vs502.out --png cp out.png WG5vs502.png Once you indexed your reference, you can query it. For example: samtools faidx reference.fasta samtools faidx reference.fasta lyrata:1-108 cd /home/reczko/bak/doc/klpno/run362/run362/klpno/pTrc8 samtools faidx pTrc8_Fasta_Sequence_02.dna pTrc8:23600-25660 > pTrc8-23600-25660.fa /data/results/tools/align/hisat/hisat2-2.1.0/hisat2-build pTrc8-23600-25660.fa pTrc8-23600-25660 cd /home/reczko/bak/doc/klpno/run362/run362/klpno/pTrc502 samtools faidx pTrc502_Fasta_Sequence_04.dna pTrc502:30300-41000 > pTrc502-30300-41000.fa /data/results/tools/align/hisat/hisat2-2.1.0/hisat2-build pTrc502-30300-41000.fa pTrc502-30300-41000 #bwa mem reczko@max:~/bak/doc/klpno/run362/run362/klpno$ ./pipKLPNO5.sh &> pipKLPNO5.log awk -f /data/images/proton2/getBWAstats.awk pipKLPNO5.log #/data/results/tools/align/mumer/MUMmer3.23/mummer -mum -b -c pTrc8/pTrc8_Fasta_Sequence_02.dna pTrc502/pTrc502_Fasta_Sequence_04.dna > 8vs502.mum /data/results/tools/align/mumer/MUMmer3.23/mummerplot -x "[0,93387]" -y "[0,100886]" -postscript -p 8vs502 8vs502.mum /data/results/tools/align/mumer/MUMmer3.23/mummerplot -x "[0,93387]" -y "[0,100886]" -postscript -p 8vs502 8vs502.out #nucmer -maxmatch -c 100 #show-coords -r -c -l nucmer.delta > nucmer.coords #show-tiling nucmer.delta > nucmer.tiling 22594 29665 67 none 1 1 (+ 22594 67) 22661 #maxGap8 start (+ 29665 67) 29732 #maxGap502 start 32026 41856 183 none - - > pTrc502 Reverse 26965 74176 1656 none - - (+ 26965 1656 ) 28621 #maxGap8 end inversion , pTrc8 coordinates: 26965 to 28621 22661 #maxGap8 start 28621 #maxGap8 end 29732 #maxGap502 start 41856 #maxGap502 end reczko@max:~/bak/doc/klpno/run362/run362/klpno/pTrc8$ ln -s *dna pTrc8.fa reczko@max:~/bak/doc/klpno/run362/run362/klpno/pTrc8$ /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc8.fa samtools faidx pTrc8_Fasta_Sequence_02.dna pTrc8:22662-28620 > pTrc8-22662-28620.fa /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc8-22662-28620.fa reczko@max:~/bak/doc/klpno/run362/run362/klpno/pTrc502$ ln -s *dna pTrc502.fa reczko@max:~/bak/doc/klpno/run362/run362/klpno/pTrc502$ /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc502.fa samtools faidx pTrc502_Fasta_Sequence_04.dna pTrc502:29733-41855 > pTrc502-29733-41855.fa /data/results/tools/align/bwa/bwa-0.7.16a/bwa index pTrc502-29733-41855.fa #IGV: noFP regions: 8:23000-26950 502:29330-42050 samtools sort KLP1-vs-pTrc502-all.bam KLP1-vs-pTrc502-all-srt samtools index KLP1-vs-pTrc502-all-srt.bam samtools sort KLP1-vs-pTrc8-all.bam KLP1-vs-pTrc8-all-srt samtools index KLP1-vs-pTrc8-all-srt.bam samtools view -b KLP1-vs-pTrc502-all-srt.bam "pTrc502:29330-42050" > KLP1-vs-pTrc502-29330-42050.bam samtools view -b KLP2-vs-pTrc502-all-srt.bam "pTrc502:29330-42050" > KLP2-vs-pTrc502-29330-42050.bam samtools view -b KLP3-vs-pTrc502-all-srt.bam "pTrc502:29330-42050" > KLP3-vs-pTrc502-29330-42050.bam samtools view -b KLP1-vs-pTrc8-all-srt.bam "pTrc8:23000-26950" > KLP1-vs-pTrc8-23000-26950.bam samtools view -b KLP2-vs-pTrc8-all-srt.bam "pTrc8:23000-26950" > KLP2-vs-pTrc8-23000-26950.bam samtools view -b KLP3-vs-pTrc8-all-srt.bam "pTrc8:23000-26950" > KLP3-vs-pTrc8-23000-26950.bam samtools flagstat KLP1-vs-pTrc502-29330-42050.bam 0 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 0 + 0 mapped (-nan%:-nan%) samtools flagstat KLP2-vs-pTrc502-29330-42050.bam 143 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 143 + 0 mapped (100.00%:-nan%) samtools flagstat KLP3-vs-pTrc502-29330-42050.bam 0 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 0 + 0 mapped (-nan%:-nan%) samtools flagstat KLP1-vs-pTrc8-23000-26950.bam 0 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 0 + 0 mapped (-nan%:-nan%) samtools flagstat KLP2-vs-pTrc8-23000-26950.bam 0 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 0 + 0 mapped (-nan%:-nan%) samtools flagstat KLP3-vs-pTrc8-23000-26950.bam 23 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 23 + 0 mapped (100.00%:-nan%) reczko@max:~/bak/doc/klpno/run362/run362/klpno$ /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 10 /home/reczko/bak/doc/klpno/run362/run362/klpno/WG5/WG5.fasta /data/images/proton2/run362/R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.KLPNC1-ecoli-res.IonXpress_017.fastq >foo cat foo | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-all-T5.bam samtools view -b -S -f 4 foo > KLP1-vs-WG-mem-all-T5-unmapped.bam samtools flagstat KLP1-vs-WG-mem-all-T5.bam 581617 + 0 mapped (100.00%:-nan%) samtools view KLP1-vs-WG-mem-all-T5.bam| grep -v XA: |wc -l 573346 /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 10 /data/results/reference/vector/univec/UniVec_Core.fa KLP1-vs-WG-mem-all-T5-unmapped.fq > foo2 cat foo2 | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-vector.bam samtools view KLP1-vs-WG-mem-vector.bam| grep -v XA: |wc -l #63099 samtools view -b -S -f 4 foo2 > KLP1-vs-WG-mem-unmapped2.bam samtools flagstat KLP1-vs-WG-mem-vector.bam /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 10 /data/results/reference/plasmid/ena/SVA.dat KLP1-vs-WG-mem-all-T5-unmapped.fq > foo2 cat foo2 | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-plasmid.bam samtools view -b -S -f 4 foo2 > KLP1-vs-WG-mem-unmapped3.bam samtools flagstat KLP1-vs-WG-mem-plasmid.bam samtools view KLP1-vs-WG-mem-plasmid.bam| grep -v XA: |wc -l 214466 # KLPN1 mapped to UniVec: 63099 # non-vector to ENA plasmids: 214466 #non-vector,non plasmids to hsa: 486153 /data/results/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx -A -o /dev/stdout -q KLP1-vs-WG-mem-unmapped3.bam > KLP1-vs-WG-mem-all-T5-unmapped3.fq (+ 63099 486153 214466) 763718 (+ 573346 763718) 1337064 #ecoli vec plas hsa mmu 573346 63099 486153 214466 24065 #tot reads (+ 771300 682069) 1453369 1453369 573346 63099 486153 214466 /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 20 /data/results/tools/snp/GATK/GATK_bundle/b37/human_g1k_v37.fasta KLP1-vs-WG-mem-all-T5-unmapped3.fq >foo cat foo | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-hsa.bam samtools view KLP1-vs-WG-mem-hsa.bam | grep -v XA: |wc -l 486153 (+ 309124 106445 581617 562917) 1560103 /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 20 /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa /data/images/proton2/run362/R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.KLPNC1-ecoli-res.IonXpress_017.fastq >foo cat foo | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-hsa.bam samtools view -b -S -f 4 foo > KLP1-vs-WG-mem-hsa-unmapped.bam samtools flagstat KLP1-vs-WG-mem-hsa.bam /data/results/tools/samtools/samtools-0.1.19/samtools view -F 256 KLP1-vs-WG-mem-hsa.bam | grep -v XA: |wc -l 1175644 /data/results/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx -A -o /dev/stdout -q KLP1-vs-WG-mem-hsa-unmapped.bam > KLP1-vs-WG-mem-hsa-unmapped.fq /data/results/tools/align/bwa/bwa-0.7.16a/bwa mem -T 5 -t 20 /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa KLP1-vs-WG-mem-hsa-unmapped.fq > foo cat foo | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - > KLP1-vs-WG-mem-mmu.bam samtools view -b -S -f 4 foo > KLP1-vs-WG-mem-mmu-unmapped.bam samtools flagstat KLP1-vs-WG-mem-mmu.bam /data/results/tools/samtools/samtools-0.1.19/samtools view -F 256 KLP1-vs-WG-mem-mmu.bam | grep -v XA: |wc -l 24065