I am trying to follow the Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying defective genomes using their DI-tector program.
Before using the program itself, it is highly recommended to filter my raw read using bwa and then samtools
Unfortunately I have no idea where to start - I have browsed official bwa and samtools sites, I have installed them using the following commands:
sudo apt-get update -y
sudo apt-get install -y bwa
I have indexed my reference genome with the following command (as I read it is required before the analysis)
bwa index sequence.fasta
Then, I have installed samtools
tar -vxjf samtools-1.9.tar.bz2
sudo apt install samtools
I wonder what will be the further steps to get these "UNMATCHED READS at the end of step i", since Di-tector program takes virus_reference genome (I have it) and these unmatched reads.
First of all I want to align my .fastq files vs
GCF_000001405.39_GRCh38.p13_genomic.fna - what will be the output file? If I got it right - I need this output file to filter with samtools, am I correct?
If I am not mistaken, the output after samtools will be the .sam file that I will have to put into a DI-tector - correct?