Perl script to read multi fasta sequence one by one
..."$key\n$fastaSeq{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; o...2222 days ago
2211 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.bai2184 days ago
Perl script to find coding regions in DNA sequences
...can not be opened\n"; exit(1); } # FASTA format: # >header containing a description of the sequ...ty (uniform), that is, 1/64. After this, # the log must be applied to obtain the log-likelihood ratio. #...2156 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...ny read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in pair...b/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM fi...d to the above call to use BWA-sampe as the paired read alignment pipeline....2125 days ago
2145 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2145 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 he...2141 days ago
Perl script to convert GFF 2 FASTA !
...## # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but containing untranslated exons) # pr...2140 days ago
2128 days ago