Results for "Reference"
Bio-Scripts
Download the genome from NCBI using bash script/command
...mkdir "G$filename" cd "G$filename" # take action on each file. $f store current file name wget --input $f #cat $f cd .. done #Reference #ftp://ftp.ncbi.nlm.nih.gov/...2525 days ago
Genetic Algorithms demonstration with word DNA in Perl
...my $pop_ref = []; # a reference to a population array...$index = sample(\@weights); # we pass a reference to the weights array here...PAN Sample module) sub sample { # get the reference to the weights array my $we...2365 days ago
- ...OVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s re...
2203 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 here my $seqfile=""...2133 days ago
- ...find matepairs split between the references. Use from-to to limit matepair distance on the same reference Filters for individual re...
2119 days ago
- ...en) 2. read mapping based (if --left and --right are given) 3. reference based (if --reference is given) Documentation at...ded, skipping read diagnostics [ INFO] 2018-07-13 14:54:34 : No reference provided, skipping comparativ...
2116 days ago
- ...(BETA Tool) Collects reference and alternate allele counts a...Compare GATK's internal pileup to a reference Samtools mpileup CheckTe...rovided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ t...
2068 days ago
Perl script to create a consensus of nucleotide sequences !
...@cons, [ sort { ($H{$b}->[$B]||0) ($H{$a}->[$B]||0) || $prefOrder{$b} $prefOrder{$a} } qw/A T G C/ ]->[0]; } return @cons; } #reference https://www.perlmonks.org/bar...2025 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1718 days ago
Samtools commands for bioinformatician !
...command) # -g : output is bcf (binary call format) file # -f : use reference genome given samtools mpileu...sal_vars.bcf > sal_vars.vcf ### normalize (realign) indels # -f : reference fasta, needed to left align a...1596 days ago
