[mira_talk] Re: less number of reads used
- From: Manoharan <manoharan.k@xxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 18 Apr 2014 11:55:04 +0530
Hi Bastien,
Thanks for the quick reply,
On Friday 18 April 2014 11:37 AM, Bastien Chevreux wrote:
On 18 Apr 2014, at 7:21 , Manoharan <manoharan.k@xxxxxxxxxxxxxxx> wrote:
Even if it is removing rrna and duplicates at least 40% data has to be used but
only 20% reads are used.
Do NOT remove duplicates except if you have a good reason to think that the
vast majority was introduced via sequencing protocol.
Is there any way to increase number of reads use age or can I have option of
switching off (digital normalization)?
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?
Either way, you do not want to switch off digital normalisation lightly … it
will most certainly make RAM and CPU usage explode. A much safer strategy is to
extract the reads which were thrown out by DN and assemble a subset of them to
get the genes they represent. Then bait out all reads not represented by those
genes and assemble normally.
If you really want to switch off DN, I’ll let you search the option yourself in
the manual :-)
B.
Thanks,
Manoharan
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