I've got a series of bins (fasta files) obtained with MetaBAT. Each file has all the contigs that were binned together. My question is if there's any way to extract the reads (from the FastQ file) mapped to each of the contigs in a bin. I have the bam mapping files.
My idea is to reassemble this reads (using something like SPAdes), to see if this results in better contigs (assuming that the reads that were binned together should come from the same genome, the assembly should be better)