Forum: Bioinformatics
01-31-2012, 12:55 PM
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Replies: 10
Views: 3,849
If you are new to NGS analysis, I could also...
If you are new to NGS analysis, I could also recommend using a commercial platform such as CLC or DNANexus for RNA-Seq analysis. CLC is a local workbench with yearly license fees (very reasonable...
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Forum: Bioinformatics
01-31-2012, 12:52 PM
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Replies: 2
Views: 1,535
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Forum: Bioinformatics
01-27-2012, 10:22 AM
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Replies: 6
Views: 3,465
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Forum: Sample Prep / Library Generation
01-23-2012, 10:21 AM
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Replies: 1
Views: 5,529
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Forum: RNA Sequencing
01-19-2012, 11:15 AM
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Replies: 6
Views: 2,668
I personally like Trans-ABySS which analyzes...
I personally like Trans-ABySS which analyzes ABySS-assembled contigs. But, you can;t go wrong with SW out of the Broad either. It may be best to try both.
But this may depend on the organism and...
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Forum: General
01-05-2012, 10:47 AM
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Replies: 5
Views: 3,100
We use several tools to call, classify, assign...
We use several tools to call, classify, assign confidence, and annotate. A good place to start is the GATK (http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit)website. ...
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Forum: Bioinformatics
01-05-2012, 10:35 AM
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Replies: 1
Views: 1,253
Hi Georgio,
I would check out CLCBio (or...
Hi Georgio,
I would check out CLCBio (or maybe another vendor - but we have used CLCBio for this). They have a great miRNA analysis pipeline. First you need to detect and trim the adapter, then...
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Forum: Bioinformatics
01-04-2012, 07:34 AM
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Replies: 1
Views: 1,924
Jonas and Jaydut,
We use SOLiD extensively...
Jonas and Jaydut,
We use SOLiD extensively here at EdgeBio and finds that when aligning transcriptome data, even more than genomic data, the alignments really matter. Just aligning with bfast or...
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Forum: Bioinformatics
12-11-2010, 07:49 AM
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Replies: 13
Views: 5,844
Asif,
This is a decision that is completely...
Asif,
This is a decision that is completely up to what the project dictates. You could try another assembler, like Celera, and see if you fill in gaps or produce a better assembly. If you want...
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Forum: Bioinformatics
12-11-2010, 07:47 AM
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Replies: 13
Views: 5,844
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Forum: SOLiD
12-11-2010, 07:36 AM
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Replies: 5
Views: 5,881
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Forum: SOLiD
08-25-2010, 06:51 AM
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Replies: 6
Views: 3,494
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Forum: SOLiD
08-22-2010, 08:57 AM
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Replies: 6
Views: 3,494
Hi EADIE,
I think it depends on how you...
Hi EADIE,
I think it depends on how you intend on processing the data. Software like bioscope and CLCBio will dynamically trim your data to remove adapters and non-miRNA sequence. They both also...
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Forum: Bioinformatics
02-18-2010, 05:14 PM
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Replies: 8
Views: 3,780
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Forum: De novo discovery
02-15-2010, 12:39 PM
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Replies: 58
Views: 52,032
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Forum: Bioinformatics
01-27-2010, 06:17 AM
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Replies: 5
Views: 1,968
Hey Scientifica, welcome to seqanswers and good...
Hey Scientifica, welcome to seqanswers and good luck with your research. I would check out http://seqanswers.com/forums/showthread.php?t=43 which details SW packages for NGS data analysis. Personal...
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Forum: Bioinformatics
01-26-2010, 06:44 AM
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Replies: 15
Views: 7,838
It looks like you are trying to generate a...
It looks like you are trying to generate a consensus fasta file from a mapping/alignment, and you are using ace only because it is what is produced by mosaik (mosaik also produces sam/bam, but not...
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Forum: Bioinformatics
01-22-2010, 12:35 PM
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Replies: 22
Views: 10,298
What type of data is it? 454 I assume, maybe...
What type of data is it? 454 I assume, maybe Sanger? There are several option out there for WGS - I don't have much experience with CAP3. Newbler or Celera Assembler could prove to be viable...
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Forum: 454 Pyrosequencing
01-22-2010, 12:25 PM
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Replies: 1
Views: 1,910
Hi Ha,
The mapper application uses a combo...
Hi Ha,
The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants...
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Forum: Bioinformatics
01-22-2010, 12:10 PM
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Replies: 15
Views: 7,838
I find the AMOS toolset...
I find the AMOS toolset (http://sourceforge.net/apps/mediawiki/amos/index.php?title=File_conversion_utilities) convenient for converting between many differnt assembly outputs/inputs.
So, in this...
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