Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regio...the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {p...1392 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.chr...mv tmp xxx.chrom.sizes gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {p...1392 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rj....6.34") -- Configuring done -- Generating done -- Build files ha...ject src/CMakeFiles/i-adhore.dir/Gene.cpp.o [ 63%] Building CXX ob...anaconda3/envs/wgd/./API/iADHoRe/gene.pm -.../testset/datasetI/arath_2_3_beta/genes.tx...1230 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input:...GI_novel_T016141 Solyc03g007600.3.1 ACGTACGTACGTACGTACGTACG EOF cat > gene_ids.txt ids_gene_ids...850 days ago
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Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF fi...to/your/file.gff'; my $genome_fasta = 'path/to/your/genome.fasta'; # Gene ID to extract my $gene_id_...121 days ago