Forum: Bioinformatics
11-04-2015, 05:30 PM
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Replies: 2
Views: 1,034
Yes, you are best to contact Geneious support...
Yes, you are best to contact Geneious support directly with any questions you have. But since I'm here I'll answer your question.
Geneious R9 includes mapper options called 'Find structural...
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Forum: Bioinformatics
05-06-2015, 11:03 PM
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Replies: 16
Views: 3,267
Geneious only provides the ability to remove...
Geneious only provides the ability to remove duplicates prior to alignment. It's probably a good idea to do so, but I don't know whether or not people typically do that.
I can see from your...
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Forum: Bioinformatics
05-04-2015, 09:22 PM
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Replies: 16
Views: 3,267
Hi Josiah,
Prior to variant calling, I...
Hi Josiah,
Prior to variant calling, I recommend you try de novo assembling all the reads that map, then map those contigs (along with any unassembled reads) to the reference sequence. By doing...
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Forum: Bioinformatics
02-26-2015, 01:58 PM
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Replies: 18
Views: 6,040
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Forum: Bioinformatics
02-25-2015, 02:03 PM
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Replies: 18
Views: 6,040
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Forum: Bioinformatics
02-24-2015, 10:32 PM
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Replies: 18
Views: 6,040
Alex shared some of his data with me to run...
Alex shared some of his data with me to run through Geneious and we corresponded a bit by email, so I thought I'd share the results with anyone else who's interested.
Geneious called the indels...
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Forum: Bioinformatics
02-18-2015, 12:21 PM
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Replies: 18
Views: 6,040
Just wondering if you've tried Geneious? It's...
Just wondering if you've tried Geneious? It's commercial software, so maybe that doesn't meet your requirements, and I'm biased since I wrote the variant caller in it, but I've never seen it fail to...
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Forum: Bioinformatics
12-15-2014, 03:14 PM
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Replies: 13
Views: 3,488
If you are working with haploid data, another...
If you are working with haploid data, another approach to get better aligned ends is to run iterative mapping where you take the consensus from the previous mapping iteration and map the reads to...
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Forum: Bioinformatics
11-18-2014, 04:24 PM
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Replies: 18
Views: 6,697
Hi Marisa,
The minimum length you keep...
Hi Marisa,
The minimum length you keep should depend on the assembler you are using. Since you intend to use Geneious, there is probably no harm in keeping all the short reads since it will...
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Forum: Bioinformatics
11-18-2014, 02:16 PM
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Replies: 6
Views: 2,081
Brian's suggestion sounds great although I'd...
Brian's suggestion sounds great although I'd tweak it to map all your reads to a combination of your contigs and any related reference mitochondria genomes you can find. And when collecting the reads...
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Forum: Bioinformatics
07-24-2014, 01:05 AM
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Replies: 3
Views: 1,921
Geneious can do it although it's commercial...
Geneious can do it although it's commercial software. There is probably some free software out there to do it, but I'm not aware of any.
A year or two ago I heard (and this might be wrong) that...
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Forum: Bioinformatics
07-22-2014, 04:31 PM
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Replies: 9
Views: 1,621
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Forum: Bioinformatics
07-22-2014, 04:15 PM
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Replies: 10
Views: 1,557
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Forum: Bioinformatics
07-10-2014, 01:52 PM
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Replies: 12
Views: 2,561
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Forum: Bioinformatics
07-09-2014, 04:52 PM
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Replies: 12
Views: 2,561
For most assembly, unpaired 50bp reads aren't...
For most assembly, unpaired 50bp reads aren't that great. But in your case, the genome is tiny and the maximum size of any repeat in it is only 12bp. So 50bp reads should be fine. I created around...
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Forum: Bioinformatics
05-08-2014, 02:20 PM
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Replies: 24
Views: 15,424
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Forum: Bioinformatics
05-08-2014, 01:01 AM
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Replies: 24
Views: 15,424
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Forum: Bioinformatics
05-06-2014, 02:55 PM
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Replies: 24
Views: 15,424
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Forum: Bioinformatics
04-29-2014, 01:54 PM
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Replies: 5
Views: 3,218
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Forum: Vendor Forum
03-13-2014, 01:31 PM
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Replies: 2
Views: 2,345
The algorithm may produce multiple circular...
The algorithm may produce multiple circular contigs as each contig may independently circularize.
As a quick confirmation I downloaded a random sample of 100 viral genomes, 24 of which are...
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