[mira_talk] Re: CNAG
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 25 Mar 2011 21:15:18 +0100
On Friday 25 March 2011 20:47:22 Tony Travis wrote:
> OK, how about attempting to assemble the smaller 'large' insert
> libraries with MIRA, and then mapping the 500bp reads onto that?
> 44x 2 x 114nt paired-end --> 500bp <--
> 8x 2 x 36nt mate-pair <-- 3kb -->
> 8x 2 x 36nt mate-pair <-- 5kb -->
> 4x 2 x 36nt mate-pair <-- 10kb -->
> Just a thought...
De-novo assemblies of reads <75bp is problematic, and <50bp is just plain
evil. At least when one expects reasonable results. 75bp starts to be nice,
and >100bp is "fun" again.
Then there's another problem: just one of the 8x coverage libraries (which
would be by far not enough anyway) of 1.8 gb with 36bp reads represents ~450m
reads! Not really much less than 800m reads.
If I made my calculations right, the whole data set has something like 1.8 to
2 billion reads.
B.
Other related posts: