Results for "Genomic Medicine"
Bio-Scripts
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" %in...2277 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releas...ation: Tools that process genomic intervals in various formats...--------------------------------------------- Metagenomics...
2068 days ago
Pack a perl program with their dependencies on Ubuntu !
...re visit here: https://www.lazoi.com/Home Comparative Genomics !!This group is dedicated to Comparative genomics ... Dramatic results have em...d interpretation of data for studies in public health and medicine. Biostatistics experts arrive...1504 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp_c...files .. Generating the correspondance map for genomic variants introduced during si...map.txt Generating reference-based vcf file for genomic...1204 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -ind...files .. Generating the correspondance map for genomic variants introduced during si...map.txt Generating reference-based vcf file for genomic...1204 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -c...files .. Generating the correspondance map for genomic variants introduced during si...map.txt Generating reference-based vcf file for genomic...1204 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inv...files .. Generating the correspondance map for genomic variants introduced during si...map.txt Generating reference-based vcf file for genomic...1204 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -tra...files .. Generating the correspondance map for genomic variants introduced during si...map.txt Generating reference-based vcf file for genomic...1204 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna943 days ago
Extract the sequences with IDs !
#sed -i 's/\_/ /g' Delta_seqID_from_lineage_report.txt seqtk subseq genomic.fna Delta_seqID_from_lineage_report.txt > Delta.fasta #Split the fasta in 11 equal sequences subsets pyfasta split -n 11 Delta.fasta844 days ago
