Results for "CAT/BAT"
Bio-Scripts
#USAGE: CI_normal(matrix[,c(x:y)],97.5) - multiple column from a normal distribution #USAGE: CI_tdist(matrix[,c(x:y)],97.5) - multiple column from a t distribution #U...2886 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101.fasta id=97 3316 mutate.sh in=mutant15CH101.fasta out=...1750 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for genome assembly summary and extract the URL...2547 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print...2546 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome_gff cd genome_gff # Look for genome assembly summary and extract...2538 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna...2346 days ago
- # bash cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "/n" > OUTFILE.fasta #awk cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",substr...
865 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo...
2142 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheteroz...2068 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles ------------------------------------------...2049 days ago
