Results for "Data mining"
Bio-Scripts
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1082 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r m...basename.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/r...1073 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh Writ...Primary input file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...stantially better assemblies for low-depth data,...1004 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda en...ironment.yml Collecting package metadata (repodata.json): done Solving environm...############# | 100% importlib-metadata-4 | 32 KB | #############...eed to manually update the taxonomy databa...951 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base).... The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samp...etected: 320 Total passing QC: 293 Data files found: Trained model:...put file written to: /home/jnarayan/RF_DATA/F...915 days ago
Installing SEVA environment in Conda !
(base) [jnarayan@hn1 SEVA_codes_and_files]$ conda env create -f SEVA.yaml Collecting package metadata (repodata.json): done Solving environm...####################################### | 100% r-data.t...866 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are available so to install we can just download this distribution and extr...851 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To use Varscan we simp...851 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data446 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745438 days ago
