Results for "Data Structure"
Bio-Scripts
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been...r', 'File::Copy', 'POSIX', 'Tie::File', 'Try::Tiny', 'Data::Dum...1207 days ago
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.1106 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r...asename.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_...1097 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh Wri...rimary input file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...tantially better assemblies for low-depth data, but...1028 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 databases...975 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...tected: 320 Total passing QC: 293 Data files found: Trained model:...ut file written to: /home/jnarayan/RF_DATA/FAST...939 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.tabl...889 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 extrac...875 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 simply...875 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data470 days ago
