Re: [AMOS-help] about tigger in minimus2 pipeline

[Ba, H. <Hen...@ag...>]

HI

I think that no contigs could overlap in any one dataset. We assembly two same mammalian species with  different reads sets (solid and illumina) and different tools .

I think it is good solution to merge two datasets.

How much contigs in one dataset is acceptable to miminus2?

Hengxing


From: Daniel Sommer [mailto:ds...@um...]
Sent: Wednesday, 16 March 2011 5:01 a.m.
To: Ba, Hengxing
Cc: amo...@li...
Subject: Re: [AMOS-help] about tigger in minimus2 pipeline

Why do you have so many contigs?   If they are all only  couple thousand base pairs you could just assemble them like they are sanger reads.

Daniel Sommer
On Mon, Mar 14, 2011 at 11:52 PM, Ba, Hengxing <Hen...@ag...<mailto:Hen...@ag...>> wrote:
Thanks
All these are contigs and no reads.

Could you tell me how to merge two large contigs sets like mine?

Hengxing


From: Dan Sommer [mailto:dds...@gm...<mailto:dds...@gm...>]
Sent: Tuesday, 15 March 2011 4:42 p.m.
To: Ba, Hengxing
Cc: amo...@li...<mailto:amo...@li...>
Subject: Re: [AMOS-help] about tigger in minimus2 pipeline

No minimus2 can not handle millions of contigs.   Are these all contigs or are you including singleton reads?

Daniel

Sent from my iPad

On Mar 14, 2011, at 7:45 PM, "Ba, Hengxing" <Hen...@ag...<mailto:Hen...@ag...>> wrote:
Hi

Anyone could help me?

I am running minimus2 pipeline to merge two large contigs sets. But the Tigger in pipeline has run 10 days and don't finish yet.

One contig set include 2376372 contigs and another  includes 1942129 contigs.

I wonder if it is difficult for Tigger to handle large datasets.

Thanks

Hengxing







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