Extract the mapped and unmapped reads !
..._End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout samtools view...649 days ago
Identify genome-wide synteny with LASTZ alignment
...r both genomes and chromosomes. RepeatMasker -pa 40 -nolow -norna -gff -xmall...stom.TE.lib_for_rice.fa AAChr1.txt RepeatMasker -pa 40 -nolow -norna -gff -xmall...01.chain.filter chainNet chr01.chain.filter -minSpace=1 AAChr1.txt.sizes FFChr1.t...576 days ago
Perl script to find inverted repeats !
...eq(); my $seq = $seqobj->seq(); # run RepeatMasker my $rm = Bio::Tools::Run::RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMasker output while...484 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str....ase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.flip; } sub find-palindromes(Str $dna, Int $min-l...a.substr($pos, $length); if is-palindrome($substring) {...484 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data477 days ago
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Raku script to find SSRs in fastq file !
...$ssr, End: $ssr, Length: $ssr, Sequence: $ssr"; } } } $fh.close; } # Replace 'your_fastq_file.fastq' with the path to your FASTQ file process...171 days ago
Bash script to calculate difference between column !
Space Separated awk '{ $5 = $2 - $4 } 1' inputput.txt > outdiff.txt Or with tab separation: awk 'BEGIN { OFS = "\t" } { $5 = $2 - $4 } 1' inputput.txt > outdiff.txt153 days ago
153 days ago