I had some environmental HiSeq data that I assembled into contigs and clustered into putative genomes. Now I wan't to go back into my BAM files and extract reads mapping back to the a list of contigs (e.g mapping back to contigs from one of my putative genomes) into a fastq file.
I can't find a way to do this though, anyone know of a way?
I can't find a way to do this though, anyone know of a way?
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