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Hi all.
This may seem a more philosophical than procedural question, but I'm gonna give it a shot here any way.
I recently got a metagenomic dataset generated on a HiSeq2500 using a TruSeq kit for library prep. This is gDNA from wild primate fecal samples. Now, I have plenty of experience with 16S- 454 and miSeq data processing, but I'm new to analyzing HiSeq metagenomic data. I have already "cleaned" my data using trimmomatics but I'm a little lost on what to do next, I've been told that I need to filter for host-origin reads first and then assemble those short reads --ALONG THESE LINES--My main objective is to make functional comparative descriptions of the microbial community rather than recovering full genomes or full-length CDS from the uncultured community, which will make assembling not necessary(?) (see http://www.microbialinformaticsj.com/content/2/1/3). Based on this, can anybody give me some opinions or pointers?
Thanks much
Andy
This may seem a more philosophical than procedural question, but I'm gonna give it a shot here any way.
I recently got a metagenomic dataset generated on a HiSeq2500 using a TruSeq kit for library prep. This is gDNA from wild primate fecal samples. Now, I have plenty of experience with 16S- 454 and miSeq data processing, but I'm new to analyzing HiSeq metagenomic data. I have already "cleaned" my data using trimmomatics but I'm a little lost on what to do next, I've been told that I need to filter for host-origin reads first and then assemble those short reads --ALONG THESE LINES--My main objective is to make functional comparative descriptions of the microbial community rather than recovering full genomes or full-length CDS from the uncultured community, which will make assembling not necessary(?) (see http://www.microbialinformaticsj.com/content/2/1/3). Based on this, can anybody give me some opinions or pointers?
Thanks much
Andy