Results for "bam"
Bio-Scripts
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.bam1278 days ago
Corona variant calling steps !
...me "$my_file" .fasta) echo $basename mkdir -p results/sam results/bam results/bcf results/vcf bwa...ed.sam samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.aligned.bam samto...1040 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
991 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt991 days ago
- ...ndex -f -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...
862 days ago
Extract the mapped and unmapped reads !
...#Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PRO...#Paired_End_Layout samtools view --threads $PROCESSORS -b -f 2 in.bam > mapped.bam samtools view -...585 days ago
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