[mira_talk] Re: less number of reads used
- From: Manoharan <manoharan.k@xxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 19 Apr 2014 13:22:05 +0530
Hi,
I switched off the DN option and assembled the reads now I am getting
76% reads showing "NO_OVERLAP" , 15% "TINY_CLUSTER" , 6% "TINY_CONTIG"
and 1.8% "SHORTONLOAD". The number of reads assembled incressed 14% more
(ie. 20 to 34% assembled reads).
Now this really means less data(i have ~30 coverage) should I have to
sequence more? & I also expect ~50MB assembled transcripts length as per
solanum family but I am getting only 8-18 (MB) for my samples i do not
know why?
Thanks & Regards,
Manoharan
On Friday 18 April 2014 11:59 AM, Bastien Chevreux wrote:
On 18 Apr 2014, at 8:25 , Manoharan <manoharan.k@xxxxxxxxxxxxxxx> wrote:
You do understand what digital normalisation does, don’t you? And why the
“unused” reads are not really unused?
My understanding on DM is if we have high copy genes it takes the subset of the
data and assemble the reads. Correct me if I am wrong.
I was worried 80% of data going unused. As per mira or DM all the expressed
genes are assembled?
Correct. Though the results with DN are worse than if you go the “split data
set and subsample” route. But the latter takes more manual work.
B.
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