Results for "align"
Bio-Scripts
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin =...'t/data/insulin.water'); my $aln = $alignin->next_aln; my $jcmatrix...ous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta',...2655 days ago
Biological Sequence handling with Perl !
...quence::Generic; use Sequence::Nucleotide::Subsequence; use Sequence::Alignment; use Carp; use strict...return ($self->length-$pos,$self->length-$pos-3*length($max)); } sub align { my $self = shift;...2187 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...2146 days ago
Long reads mapper bash script !
...cho "NGMLR:Please specify reads type: ont, pacbio" fi elif [ $toolName == "graphmap" ]; then echo "Mapping with $toolName" $graphMapLoc align -r $refFasta -d $longReads -t...2128 days ago
Installing Platypus on Ubuntu !
...x-x86_64-2.7/c/tandem.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cerrormodel.so cythoning cython/calign.pyx to cython/calign.c /home/urbe/anaconda3/envs/...2025 days ago
Samtools commands for bioinformatician !
...dels with no frequency threshold # omit -v parameter bcftools call -c sal_vars.bcf > sal_vars.vcf ### normalize (realign) indels # -f : reference fasta, needed to left align and normalize bcftools norm...1609 days ago
Bash script to alignment of short reads against reference genome !
...0413.raw.sorted.bam SRR1770413.bam ##Breaking it down by line: #alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and al...1565 days ago
- (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 --...
1448 days ago
