Results for "RefSeq"
Bio-Scripts
Download the genome from NCBI using bash script/command
...ungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' |...ant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt' |...ozoa curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/protozoa/assembly_summary.txt...2532 days ago
Download the gff files from NCBI using bash script/command
...ungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' |...ant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt' |...ozoa curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/protozoa/assembly_summary.txt...2523 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, load it, # if not, install and load it if("ggplot2" %i...2285 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...clustalReads.pl genome.fa > HammingDist.txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($A...eqIds[$cnt]; print "$chr\t@$SeqIds[$cnt]\t"; print $ofh ">$chr\n$refSeq->{$chr}{seq}\n>@$SeqIds[$cnt]...2141 days ago
Create random 10000 SNPs in genome !
...) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp_c...ariants introduced during simulation: simuSNP.refseq2simseq.map.txt Generating...ariants introduced during simulation: simuSNP.refseq2simseq.SNP.vcf [Sun Jan 10 1...1211 days ago
Create random 1000 INDEL in genome !
...) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -ind...iants introduced during simulation: simuINDEL.refseq2simseq.map.txt Generating...iants introduced during simulation: simuINDEL.refseq2simseq.INDEL.vcf [Sun Jan...1211 days ago
Create random 1000 CNVs in genome !
...) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -c...ariants introduced during simulation: simuCNV.refseq2simseq.map.txt Generating...ariants introduced during simulation: simuCNV.refseq2simseq.CNV.vcf [Sun Jan 10...1211 days ago
Create random 5 inversions in genome !
...) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inv...ariants introduced during simulation: simuINV.refseq2simseq.map.txt Generating...ariants introduced during simulation: simuINV.refseq2simseq.inversion.vcf [Sun...1211 days ago
Create random 2 translocations in genome !
...) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -tra...iants introduced during simulation: simuTRANS.refseq2simseq.map.txt Generating...iants introduced during simulation: simuTRANS.refseq2simseq.translocation.vcf [...1211 days ago
Command line to download blast database / protein
...h.gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq #First run this to downloa...944 days ago
