Results for "positions"
Bio-Scripts
...is the PNG file created. default: ___.png A database file containing the positions of words of enc...2707 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2482 days ago
Plot the density of genes in R
...talled.packages())){ library(ggplot2) } else { install.packages("ggplot2") library(ggplot2) } # import a text file with gene positions # columns should be: chr, po...2298 days ago
- ...BAM file to multiple BAMs. UmiAwareMarkDuplicatesWithMateCigar (Picard) (BETA Tool) Identifies duplicate reads using information from read positions and UMIs. UnmarkDuplica...
2089 days ago
Samtools commands for bioinformatician !
...e: returns count of depth at each position. input should be sorted ### count depth at each position and put it into a txt file # -a : at all positions samtools depth -a sorted_dup...1616 days ago
Perl script to find inverted repeats !
...rt+1); if ($rm_strand eq "-") { $rm_seq = reverse_complement($rm_seq); } print "Inverted repeat found at positions $rm_start-$rm_end: $rm_seq\n"...439 days ago
- #!/usr/bin/env Rscript library(RCircos) # usage: Rscript make_circos.r # parse args args = commandArgs(trailingOnly=TRUE) sv.file
313 days ago
