CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gs...);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe...iasMetrics.jar) R=data/Cdiff078.fa I=aln-pe.mapped.sorted.$i.bam O=aln-pe...2057 days ago
Setting up falconUnzip conda environments for genome assembly !
...vs/denovo_asm added / updated specs: - pb-assembly T...180 KB conda-forge pyopenssl-18.0.0 |...34 KB conda-forge intel-openmp-2019.1 |...27h3dfced4_0 openssl: 1.0.2p-h...2043 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2025 days ago
Backward Elimination with Python
...maxVar = max(regressor_OLS.pvalues).astype(float) if maxVar > s...if (regressor_OLS.pvalues[j].astype(float) == maxVar):...ars = len(x[0]) temp = np.zeros((50,6)).astype(int) for i in range(0, n...2008 days ago
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\w+)/; $cou...1954 days ago
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Palindrome Simulation commands !
...umina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/seqtk mergepe paired_dat1.fq paired_dat2.fq > interleavedPE.fq 3322 ~/Tools/seqtk/seqt...1789 days ago
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Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use...$chr_set!\n"; } sub touch { my ($fn, $seq) = @_; open FILE, ">$fn" or die $!; system ("augustus --species=caenorhabditis --outfile=...1739 days ago