Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/f...urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/gra...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.ou...= "pacbio" ]; then $ngmlrLoc -t $thread -r $refFasta -q...2179 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...$_; } } $map{$id} = $seq; close(IN); return \%map; }2190 days ago
2184 days ago
2183 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, '2182 days ago
2180 days ago
1573 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting ob...ges/porechop/porechop.py to porechop.cpython-36.pyc byte-com...-v VERBOSITY, --verbosity VERBOSITY...2163 days ago
2156 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C...= do{ local $/; }; chomp $in; print $in; for my $p1 ( 1 .. le...ess substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1 };...*2; my $ed=($st+$sLen)-1; print "$st\t$ed\t$sLen\t$val\n";...2156 days ago