Basicaslly the idea we have is to map our metagenomeic reads to a file containing all isolated genomes from the environment. Then remove the mapped reads from the original reads files (of which there are 12 due to 6 paired end runs). I currently have mapped the reads to the reference genomes using BOWTIE2 but am now stuck on how to remove just these reads and to remove them from all the files. I assume some form of comparison and then grep removal into another file would work but am still new to coding so would appreciate any help people can provide.
Thanks,
Tom
Thanks,
Tom
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