Perl script to find coding regions in DNA sequences
...ilesequence")) { print "dnaloglkh.pl: the file $filesequence can not be opened\n"; exit(1); } # FASTA format: # >header containing a description of the sequence # AGACTGA...2154 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...needs to be aligned in paired read mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obt...pipeline. https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py2123 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2182 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/n...2143 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa >...2139 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here...2139 days ago
Perl script to convert GFF 2 FASTA !
...gene.fasta" ); my $outfile_upstream3000 = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type description ###### # cds - translated...2138 days ago
2136 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, '2124 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 is a bash scrip to map your long reads and make it...2121 days ago