Results for "Data"
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.1067 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS=...me.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_genome/sequences.fasta re...1058 days ago
Tadpole is 250x faster than SPADes assembler !
...in= Primary input file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...can produce substantially better assemblies for low-depth data, but they are very slow for l...989 days ago
Installing Covid19 Environment !
...vid19-environment.yml Collecting package metadata (repodata.json): done Solving environm...###################### | 100% importlib-metadata-4 | 32 KB | #############...u still need to manually update the taxonomy databases before Krona can generat...936 days ago
Run Pango on your multifasta file !
...satisfied. The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samp...quences detected: 320 Total passing QC: 293 Data files found: Trained model:...0:09 Output file written to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv (pa...900 days ago
Installing SEVA environment in Conda !
...es_and_files]$ conda env create -f SEVA.yaml Collecting package metadata (repodata.json): done Solving environm...########################################################## | 100% r-data.table-1.14.0 | 2.0 MB | #...851 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 dist...836 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...836 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data431 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 PRJNA880745423 days ago
