Pack a perl program with their dependencies on Ubuntu !
...find the test script web.pl at https://bioinformaticsonline.com/snippets/view/41440/perl-script-to-reads-an..._gaq.push(['_setAccount', 'UA-42478605-1']); _gaq.push(['_trackPageview']); (function() {...1503 days ago
Corona variant calling steps !
...mkdir -p results/sam results/bam results/bcf results/vcf bwa mem trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam samtools view -S -b results/sam/$basename.a...1037 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.txt988 days ago
942 days ago
Extract the mapped and unmapped reads !
PROCESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4...> unmapped.bam #Paired_End_Layout samtools view --threads $PROCESSORS -b -f 2...582 days ago