Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1643 days ago
Samtools commands for bioinformatician !
...use reference genome given samtools mpileup -g -f sal_ref_sej.fasta sal_sej_sorted.bam.bam > sal_vars.bcf ### calling snp and indels # -c : find snp # -v : output only poten...1630 days ago
Pack a perl program with their dependencies on Ubuntu !
...etting up libpar-perl (1.015-1) ... Setting up libpar-packer-perl (1.041-2) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... #you can find the test script web.pl at htt...1539 days ago
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Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...y', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin', 'File::Remove',...'Getopt::Long', 'Statistics::R', 'Math::Round', 'File::Find', 'Bio::DB::Taxonomy',...1188 days ago
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Perl script to check modules installed !
...y', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin', 'File::Remove',...'Getopt::Long', 'Statistics::R', 'Math::Round', 'File::Find', 'Bio::DB::Taxonomy',...1183 days ago