Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/01/2020, 05:30:00 ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00...1418 days ago
Command to sort the bed file !
#Command to sort the bed file sort -V -k1,1 -k2,2 test.bed1405 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1381 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...nome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort | bedto...1381 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...file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort -g xxx.chrom.sizes | bedto...1381 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA...#Match FASTA headers in two different multi-FASTA files $ awk 'NR=FNR{a[$0];next}$...$0}' input1.fasta input2.fasta #Merge all FASTA files in a directory into a single...1373 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -...021] Simulation completed! :) [Sun Jan 10 16:05:57 2021] Generating output files .. Generating the correspo...1227 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa...021] Simulation completed! :) [Sun Jan 10 16:14:00 2021] Generating output files .. Generating the correspo...1227 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome....021] Simulation completed! :) [Sun Jan 10 16:24:20 2021] Generating output files .. Generating the correspo...1227 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa...021] Simulation completed! :) [Sun Jan 10 16:30:40 2021] Generating output files .. Generating the correspo...1227 days ago