4. SILVA wget and RNA to DNA

wget https://www.arb-silva.de/fileadmin/silva_databases/release_138.1/Exports/SILVA_138.1_LSURef_tax_silva.fasta.gz
wget https://www.arb-silva.de/fileadmin/silva_databases/release_138.1/Exports/SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz

gunzip SILVA_138.1_LSURef_tax_silva.fasta.gz
gunzip SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz

## Running following script to change U to T.

#!/bin/bash
#SBATCH --job-name=SILVA_RNA2DNA
#SBATCH --partition=highmem_p
#SBATCH --ntasks=1
#SBATCH --mem=100gb
#SBATCH --time=20:00:00
#SBATCH --output=RNA2DNA.%j.out
#SBATCH --error=RNAtoDNA.%j.err

cd $SLURM_SUBMIT_DIR

more SILVA_138.1_SSURef_NR99_tax_silva.fasta | awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}'| sed 's/\t/\n/g'| while read L; do echo $L; read L; echo "$L" | tr "U" "T"; done > SILVA_138.1_SSURef_NR99_tax_silva_DNA.fasta
more SILVA_138.1_LSURef_tax_silva.fasta | awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}'| sed 's/\t/\n/g'| while read L; do echo $L; read L; echo "$L" | tr "U" "T"; done > SILVA_138.1_LSURef_tax_silva_DNA.fasta


## Then manually removed the header with different symbol with nano filename.fasta

Finally combine two fasta files in one signle file.

cat SILVA_138.1_* > SILVA_138.1_LSURef_SSURef.fasta