Dear all, I am trying to do read mapping to construct cp genomes using a reference genome and performing the mapping with bwa-mem.
I am running this command
bwa mem -M -B 4 $REF $R1 $R2 > output.bam
-M to mark shorter split as secondary and -B 4 for mismatch penalty. I have two questions:
1)after I have run bwa and my reference genome fasta file is 160kb and and my fastq files are 2.70 GB should I get a bam file of 5 GB or should it be smaller?
2) when I try to convert the bam file into a fasta using samtools is there a way to have the reference genome on the top and then the reads? how should the fasta file look like in order to then use it to annotate the genomes for example in Geneious?
I hope my question are not too vague or basic. thanks a lot