On Tue, Nov 25, 2014 at 09:29:35AM -0500, dan miller wrote: > Dear Sebastian Boisvert, > I just came across your publication from 2012 in "Genome biology" and > found it (like many other people apparently) extremely interesting.
Thank you. I too find metagenomics fascinating. > I would like to try to assemble some meta-data using meta-RAY. However i > am analyzing meta-transcriptome and not meta-genome data. In principle, it should work. However, RNA splicing events / alternative transcripts are not something that will work out of the box. > in principle i would think that the problems for de-novo aseembly are > similar in both cases but rather harsher in the case of metatranscriptome > (wouldn't you agree?) I suppose so if you limit the scope to bacterial transcription. Virus transcripts can overlap with each others, and eukaryotic transcripts are more complex since eukaryotic genes have introns and exons and that the same set of exons can lead to different transcripts. > My question is therefore weather your tool is suitable for the de-novo > assembly of meta-transcriptome data sets? I think if it worth a try if the size of your data is large enough that you can't use others tool more tailored for this problem. > The size of a typical data set is between 210 million to 3 billion X > 100-bp paired reads (same magnitude you described for the artificial data > sets in your paper). As for the variability of the samples- i performed > some clustering (100% identity) on one data set and found that it was > extremely reduced to about 10% of original sample size. i do not know > whether this is the case for all my data-sets. > I wouldn't like to bother you with further technical details now (unless > there is anything else you would like to know?) Mailing lists are where people discuss technical details. No problem here. > so i will cut it here :) > Your advice will be highly appreciated, hope you can find the time to > reply. > thanks in advance! > Dan Miller ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
