Results for "short reads mapping"
Bio-Scripts
P2872 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod d...e} && $targetSeqs{$tName}){ my %meta = (); my $short...= ($tSize < $qSize) ? 1 : 0; my $longTarget = (1 - $shortTa...2309 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2265 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!defi...2155 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X=...
2211 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files...hlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining...in one go. An example call for mapping with this script is python reads_to_ctg_map.py /...hlin/BESST/blob/master/scripts/reads_to_ctg_map.py2125 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>...2134 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqTyp...building a k-mer catalog from reads) -- ------------------------..._normalization/tmp_normalized_reads Normalization complete....6.6/trinity_out_dir/chrysalis/readsToComponents.out > /home/urbe/...6/trinity_out_dir/partitioned_reads.f...
2128 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-du...split into individual reads --split-spot...Split spots into individual reads Full Spot Filters...ce Filters for individual reads Applied only with --spl...reads a...
2127 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This i...me == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...== "ngmlr" ]; then echo "Mapping with $toolName" if [ $readsType == "ont" ]; then $ngm...2123 days ago
