Results for "Sam"
Bio-Scripts
Bash script to alignment of short reads against reference genome !
....fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam...ive the reads the read group K12 and the sample name K12" #reference and...le the second mate. #conversion to BAM: samtools view -b - --- this reads...1580 days ago
To convert just one specific read group to fastq
...s -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM file for each SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=reads/...1563 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.bam1304 days ago
Corona variant calling steps !
...ame=$(basename "$my_file" .fasta) echo $basename mkdir -p results/sam results/bam results/bcf results/vcf bwa mem trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam samto...1065 days ago
- ...or_mapping.btindex bowtie2 -x toy_dataset_contig_for_mapping.btindex -f -U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam samtools sort toy_dataset_mapped_...
888 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam838 days ago
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