Results for "N"
Bio-Scripts
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa read...c=/home/urbe/Tools/graphmap/bin/Linux-x64/graphmap minimap2L...n echo "Mapping with $toolName" $lamsaLoc index $refF...$toolName == "graphmap" ]; then echo "Mapping with $toolN...2177 days ago
Perl subroutine to read genome/reads fasta file !
...{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open fi...while(){ chomp; if($_ =~ /^>/){ if(defined $id && defined $seq){...q=$seq.$_; } } $map{$id} = $seq; close(IN); return \%map; }2188 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory...5 -L 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM...mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trini...t_dir/read_partitions/Fb_0/CBin_180 Monday, July 9, 2018: 11...
2182 days ago
- ...Usage: ./fastq-dump [options] [...] ./fastq-dump [options] INPUT -A|--accession...data are present --aligned...Legacy 3-file splitting for mate-pairs:...report generation (if implemented). One of...
2181 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2180 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate...Steve Kelly DESCRIPTION: Analyse a de-novo transcriptome...comma-separated --reference= Reference proteo...media/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trin...
2178 days ago
- # list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5daup/download", "ERR45...ERR458495":"https://osf.io/2wvn3/download",...ownload_reads: output: "rnaseq/raw_data/{sample}.fq.gz"...
1571 days ago
Installing Porechop on Ubuntu !
...Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting objects: 1579, done. rem...arcodes] [--untrimmed] [--discard_unassigned...Comma-delimited string of alignment scores: match,...2161 days ago
- set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0.18/reapr WadinetaGapFilled.gapfilled.iterati...a echo "[REAPR pipeline] Running preprocess" /home/urbe/T...R1.fastq /home/urbe/DATA/OriginalReads/ANature/GC027568.15112...
2154 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; }; chomp $in;...-2 ) { next unless substr( $in, $p1, 1 ) eq $invert{ substr...if( $pals ) { my $val=substr( $in, $p1-$pals, ($pals+1)*2 );...2154 days ago
