Results for "SAM tool"
Bio-Scripts
#!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {print $0}' deduped_MA605.coverage >...2002 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1724 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converti...sam # -o : output file name samtools view -b -S -o sal_sej.bam s...### results into txt file samtools depth /path/to/sorted_bam.ba...1601 days ago
Bash script to alignment of short reads against reference genome !
...RR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam...ds the read group K12 and the sample name K12" #reference and...nd mate. #conversion to BAM: samtools view -b - --- this reads SAM...341549_2.fastq.gz \ | samtools view -b - >SRR341549.raw.min...1557 days ago
To convert just one specific read group to fastq
...Generate a separate BAM file for each SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=reads/...Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam...echo "" echo "SAM file header:" samtools view -H all.bam echo ""...1540 days ago
Pack a perl program with their dependencies on Ubuntu !
...t health. Newest members Samantha Filipów@samfil Nalesh G Jadhav@mas...s Neelam Jha@neelam GSP4PDB: a web tool to visualize, search and expl...eelam Jha yesterday GSP4PDBwebtoolvisualizesearchexploreprotein-...1509 days ago
- #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight tool for processing biological dat...
1400 days ago
Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1282 days ago
Corona variant calling steps !
...$basename mkdir -p results/sam results/bam results/bcf resul...astq_small/$filename > results/sam/$basename.aligned.sam samtools view -S -b results/sam/$base...bam/$basename.aligned.bam samtools sort -o results/bam/$basenam...t_Results_of_COVID_gz/ bcftools merge results/bcf/*.vcf.gz -...1043 days ago
- ...-U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam samtools sort toy_dataset_mapped_species1.bam -o toy_dataset_mapped_species1_sorted.bam samtools index toy_dataset_mapped_spe...
865 days ago
