[mira_talk] genomic data with "-job=est" ???
- From: "visam" <teutara@xxxxxxxxxxx>
- To: "Mira Talk" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 31 May 2012 13:27:18 +0300
Hi there,
Please do not pull your swords immediately, nor ignore.
I am doing experimental assemblies with a low coverage 454 Titanium data (a
plant). After many assemblies with different settings, and having primers
designed for each and all of them, I wanted to test out the primers that
occurred in most of the assemblies. So I had more than a hundred primers in wet
lab tested, and all of them are working flawlessly.
Since I now which primers yield transcripts, I filtered those and tried to find
those little sequences in my assemblies. But I could not find all of them in an
assembly, while I should find. I thought that having more primers mapped to an
assembly might present a higher quality assembly, but for now can not demo.
The thing is, when I - I do not now why I did that, maybe it thought it would
be fun or something- told mira those reads that I have are ESTs (-job=est), and
have an assembly, I mapped the primers I have in hand, and baaam.. ALL of the
primers mapped.
So, can you please shed some light? I am thinking in a way that does not make
sense by mapping the primers? How or why I get those primers mapped to the EST
assembly?
Best,
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