Bioinformatics(생정보학) 썸네일형 리스트형 WES alignment pipeline #!/bin/bash # This script is to align DNA seq reads to reference genome GRCH38 and to conduct removing PCR duplicates # The softwares and parameters in this pipeline were refered from TCGA bioinformatics pipeline # https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#dna-seq-alignment-command-line-parameters # In case of trimming adaptor sequence, I determi.. 더보기 TCGA somatic maf files #===========================================# This script is to make missense variant file for Single nucleotide variants# Its output file will not evaluate other variants including nonsense mutation and frameshit# contatining informations are gene, entrezID, protein position, ref aminoacid/alt aminoacid#===========================================library(osjpkg);install_and_attach_lib()# Load TC.. 더보기 VEP variant location point mutation의 경우는 원본 VCF파일과 동일함insertion의 경우는 원본 VCF파일의 coordinate에서 +1까지로 만듬(ex : chr1:1468592 C/CG (VCF) -> chr1:1468592-1468593 -/G (VEP)) deletion의 경우는 원본 vcf파일의 coordinate에서 +1(ex : chr1:1741091 CT/C (VCF) -> chr1:1741092 T/- (VEP)) 더보기 VEP for loop bash file #!/bin/bashecho 'This is to run VEP version 93 cache 94 GRCh37'# Program pathVEP_path=/mnt/bigHDD/resource/ref_and_tools/tools/ensembl-vep/vepdir_cache=/mnt/bigHDD/resource/ref_and_tools/tools/ensembl-vep/caches/homo_sapiens_mergedfasta_file=/mnt/bigHDD/resource/ref_and_tools/reference/human/ensembl/GRCh37.75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa# Get current directory's VCF filesls | g.. 더보기 Cancer subclone calculation https://cran.r-project.org/web/packages/expands/vignettes/expands.pdf 인용 논문https://www.nature.com/articles/s41591-018-0086-7#Sec10 더보기 protein localization관련 db GeneCards에서 사용하는 dbhttps://compartments.jensenlab.org/Downloads Riken에서 curation한 것들 좀 오래됨.http://locate.imb.uq.edu.au/downloads.shtml Human Protein Atlas DBhttps://www.proteinatlas.org/about/download 더보기 RNAseq cufflinks로 나온 genes.fpkm_tracking파일 합치기 #!/bin/bash# This script is to quantify samsung's RNAseq data#$ -S /bin/bash#$ -N bulkCombine#$ -cwd #========================================# Set up parameters#========================================out_dir=/path_to_FPKM_file_dir/suffix_1=/genes.fpkm_trackingcom_dir=/path_to_FPKM_dir_header/header_dir #=======================================# Get file prefix#==================================.. 더보기 STAR alignment script in cluster #!/bin/bash# This script is to align samsung's single cell RNAseq data using STAR#$ -S /bin/bash#$ -N singleRseq#$ -cwd #========================================# Set up parameters#========================================ref_genome_dir=/home/osj118/ref_and_tools/samsung_GTFref_GTF=/home/osj118/ref_and_tools/samsung_GTF/ensGene.20151111.new_name.gtfstar_path=/home/osj118/ref_and_tools/star_aligne.. 더보기 이전 1 ··· 3 4 5 6 7 8 9 ··· 12 다음