I wanna perform a Viral metagenomics study of transcriptomics data. So I need to extract the unmapped reads and assemble them. My questions are :
1- do this script of samtools suit my purpose :
samtools view -b -@ 8 -f12 sample.bam > sample_unmapped.bam
2- About the assembly, do you have a suggestion for me, please?
3- For the annotation, is blast database suitable?
Thanks in advance