[mira_talk] Re: less number of reads used
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 18 Apr 2014 08:07:00 +0200
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?
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.
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