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Forum: RNA Sequencing 07-23-2012, 11:17 PM
Replies: 2
Views: 3,167
Posted By odysseus
Hi, You can refer to MATS...

Hi,
You can refer to MATS (http://rnaseq-mats.sourceforge.net/). It can automatically detect and analyze alternative splicing events corresponding to all major 5 types of alternative splicing...
Forum: Bioinformatics 11-03-2010, 06:02 PM
Replies: 10
Views: 4,091
Posted By odysseus
In my experience, SOAPdenovo better than ABySS...

In my experience, SOAPdenovo better than ABySS for assembling large Solexa read set.
I successfully completed assembly using SOAPdenovo. :-)
Forum: Bioinformatics 08-23-2010, 02:10 AM
Replies: 3
Views: 5,305
Posted By odysseus
Hi~ 1) Are contigs created from paired-end...

Hi~

1) Are contigs created from paired-end reads? If they are, you should assemble them using paired-end assembly function of Newbler. After paired-end assembly, you can get a set of scaffold.
...
Forum: Bioinformatics 08-19-2010, 06:53 PM
Replies: 10
Views: 4,091
Posted By odysseus
Thanks for all the comments everyone. I'm going...

Thanks for all the comments everyone. I'm going to use ABySS.
Forum: Bioinformatics 08-18-2010, 09:44 AM
Replies: 10
Views: 4,091
Posted By odysseus
De novo assembler for 300 million Solexa reads

Hi~ all ^^

I'm currently trying to assemble genome sequence and I have about 300 million Solexa reads (Paired-end; 220bp insert size).

When I using Velvet for assembling, I've got an error as...
Forum: Bioinformatics 03-21-2010, 09:05 PM
Replies: 0
Views: 1,430
Posted By odysseus
Question How can I determine order of scaffolds from de novo sequencing?

Hi all,

I've got about 15,000 scaffolds from de novo sequencing using 454 titanium.
I want to determine order of them using EST and BAC-end sequence data.
Now I'm searching for bioinformatics...
Forum: Introductions 03-21-2010, 05:45 AM
Replies: 0
Views: 1,513
Posted By odysseus
Question How can I determine order of scaffolds from de novo sequencing?

Hi all,

I've got about 15,000 scaffolds from de novo sequencing using 454 titanium.
I want to determine order of them using EST and BAC-end sequence data.
Now I'm searching for bioinformatics...
Forum: Bioinformatics 08-06-2009, 02:08 AM
Replies: 236
Views: 615,026
Posted By odysseus
Exclamation Thanks for your useful post. I’m interested...

Thanks for your useful post.

I’m interested in ABySS and I installed it on my linux server.
However, I knew it does not use a reference genome, as it is a de novo assembler.
I think it should be...
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