Results for "mapped"
Bio-Scripts
P2869 days ago
Create genome scaffolding with Perl
...e code use Getopt::Long qw(:config auto_version auto_help pass_through); our $VERSION = "1.00"; =head1 NAME psl_scaffolder.pl - use self-mapped PSL file to scaffold a genome...2306 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^...nt $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped...trics.jar) R=data/Cdiff078.fa I=aln-pe.mapped.sorted.$i.bam O=aln-pe.mapped...2001 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam...verting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### conv...ailed reads # and rows: total reads, duplicates, mapped. samtools flagstat sorted_du...1600 days ago
Extract the mapped and unmapped reads !
...ls view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout sa...view --threads $PROCESSORS -b -F 2 in.bam > unmapped.bam...588 days ago
