Results for "read depth"
Bio-Scripts
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open...while() { chomp; $ids{$_} += 1; } close FILE; local $/ = "\n>"; # read...2093 days ago
- ...ols that count coverage, e.g. depth per allele ASEReadCount...Calculate the fraction of reads coming from cross-sample con...etting MAPQ to 0 for unmapped reads ClipReads...1R2 ). AnnotateVcfWithBamDepth (Interna...
2072 days ago
- library(vcfR) # Input the files. vcf
2057 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2052 days ago
Generate simulated polyploid genome !
...sta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads --depth 50 toyheterozygous3percent.fa...2050 days ago
- #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗...fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~...fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~...fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~..../src/shared concentrations.o ReadC...
2023 days ago
- #!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA6...
2001 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while()...
1602 days ago
Samtools commands for bioinformatician !
...sej.bam | less ### count reads (-c) by flag specified samt...sults into txt file samtools depth /path/to/sorted_bam.bam > /p...t ### note: returns count of depth at each position. input shoul...one liner to count coverage breadth samtools depth -a sorted_du...1600 days ago
- $ sudo apt install npm Reading package lists... Done Building dependency tree Reading state information... Done...e node-pseudomap node-qs node-read node-read-package-json node-r...tu bionic/universe amd64 node-read all 1.0.7-1 [4,572 B]...ously unselected package node-read....
1550 days ago
