Results for "Arabidopsis data"
Bio-Scripts
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the req...', 'File::Copy', 'POSIX', 'Tie::File', 'Try::Tiny', 'Data::Dumper', 'File::Basenam...1212 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.1111 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...1102 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/...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 they are very slow for l...1033 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vi...ironment.yml Collecting package metadata (repodata.json): done Solving environm...############# | 100% importlib-metadata-4 | 32 KB | #############...eed to manually update the taxonomy databases before Krona can generat...980 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pango...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/FASTA/lineage_report.csv (pa...944 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.table-1.14.0 | 2.0 MB | #...894 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...880 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 need to dow...880 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data475 days ago
