Results for "region"
Bio-Scripts
Python script to download covid genome !
...= seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-region'] == "complete": nm = x[...1133 days ago
Create genome scaffolding with Perl
...affold_", # prefix for contig names "pid" => 90, # percent ID threshold "trimlimit" => 50, # max number of overlapping bases outside match region }; GetOptions($projOpts...2305 days ago
Plot custom gene density with R
library(karyoploteR) pp2246 days ago
Perl script to convert GFF 2 FASTA !
...ds translated (includes a * as the stop codon) # gene - the entire gene sequence (including UTRs and introns) # upstream3000 - the 3000 upstream region of the gene (likely including...2136 days ago
- ...t --aligned Dump only aligned sequences --unaligned Dump only unaligned sequences --aligned-region Filter by position on genom...
2123 days ago
Perl script to break the contigs by 'N'
...$seq; #now all bases are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stores a hash from the conti...minNlen) { my $end=$i; my $ini=$end-$n+1; push(@regions,"$ini $end"); } $n=0...2059 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | aw...1362 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.c...1362 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...1/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wfo...1/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wfo...1200 days ago
- ...lt = 22.0 -g Gapped [T/F] default = T -S Start of required region in query [Integer] default = 1 -H End of required region in query (-1 indicates end of...
947 days ago
