Sorry for posting a simple question but although I have worked with some assembly before, I never worked with data at the whole genome scale and I would like to ask for some advice.
I followed this tutorial on biostairs: Reference Assembly - Mapping Reads To A Reference Genome but I ended up just converting my mapped to fastq (so I did not obtain mpileup files as I wasn't doing any variant calling - although this will likely change once I get my first basic pipeline working).
My question now is...what can I do with my mapped reads? Most tutorials like the one I linked sort of just end off after gathering bam files or converting them into fastq files of mapped reads and then it sort of just stops there.
Looking at other biostars forums looks like the next thing I need to do is to annotate my mapped reads - but how do I do that? I have an annotation.gff file but I really don't understand how do I link my bam files to the annotation.gff file. The coordinates in the bam file should be identical to the .gff file right? Am I supposed to annotate my bam files and append more information into it? And if so, is this something I can do with samtools or something similar?
My end goal right now is to visualize my assembly and get information on how many genes mapped to the ref genome, which genes mapped (i.e. annotations!), and just overall quality of the mapping. But I just don't understand how to get the information from the annotation.gff file onto my mapped reads in my bam file (which btw are all still separate sequences in a read1.fastq and read2.fastq file). Any tips/advice is much appreciated. Thank you for reading!