<div dir="ltr">Under "Run the first round of diginorm", on the second bit catching the single reads, I think if you exclude the hash size, it will use the defaults (which aren't that useful), I'd suggest putting size in here consistent with the first one. I believe the default is 1e9 which is inconsistent with the 5e8 anyways.<div>
<br></div><div>-a</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 21, 2013 at 1:35 PM, Adina Chuang Howe <span dir="ltr"><<a href="mailto:howead@msu.edu" target="_blank">howead@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Just a few minor comments on metagenome assembly tutorial.<div><br></div><div>1) I like to have the report printing with the -R option but maybe it is excluded here for simplification, but I also like to see it to see how things are proceeding (e.g., how much longer things will take)</div>
<div><br></div><div>2) Digression: For metagenome assembly, the protocol "as is" is what I usually run if I have a pretty large insert size and my reads aren't expected to overlap. For the more complex environments, I've opted to have more overlapping reads (smaller insert sizes) and do a merge of these paired prior to any diginorm, assembly, etc. I dont know if needs to be in the manual, but I wanted to bring it up as a distinguishment on what I would at least recommend based on library prep. In the case that I have a lot of merged pairs (>80%), I run those through diginorm first and then grab the orphans and put them in as paired ends (no merge). This leaves trimmomatic orphans as bastardized files and a p.i.t.a to deal with -- since they typically make up less than 1% of my reads, I usually exclude trimmomatic se files from any other analysis.</div>
<div><br></div><div>3) Do we need more explanation of what -V is, i.e., just put in that we're only trimming from high coverage and not everything? I had to go look at the code to understand the new option.</div><div>
<br></div><div>Probably more to come as I run through this...but it looks nice!</div><div><br></div><div><br></div></div>
</blockquote></div><br></div>