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.bai2198 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 her...2155 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -form...2154 days ago
2142 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, '2140 days ago
Long reads mapper bash script !
...er name and parameter !" fi echo "Getting files ready for visualization !" $samtools view -Sb $fileName.out.sam | $samtools sort -m 4G -@$thread -o $fileName.sorted.bam - && $samtools index -@...2138 days ago
Perl script to create a consensus of nucleotide sequences !
...%H = ( A=>[], T=>[], C=>[], G=>[] ); s/\s//g for @mi; my ($w) = sort {$b $a} map {length} @mi;...>2, C=>3, G=>4 ); foreach my $B ( 0 .. $w-1 ){ push @cons, [ sort { ($H{$b}->[$B]||0) ($H{$a}-...2047 days ago
Perl script to count occurrence of a character !
...gs; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\w+)/; $count_of{$val[13]}++; } foreach my $word ( sort { $count_of{$a} $count_of{$b...1916 days ago
1849 days ago
Samtools commands for bioinformatician !
...mand) samtool view sal_sej.bam | less ### sort reads by flag specified and s...samtools view -q 42 -c sal_sej.bam ### sorting bam file by genome positio...igned.vcf ### show alignment # first arg is sorted bam file # second arg is r...1618 days ago