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Search: Posts Made By: Matt Kearse
Forum: Bioinformatics 11-04-2015, 04:30 PM
Replies: 2
Views: 988
Posted By Matt Kearse
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...
Forum: Bioinformatics 05-06-2015, 10:03 PM
Replies: 16
Views: 3,201
Posted By Matt Kearse
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...
Forum: Bioinformatics 05-04-2015, 08:22 PM
Replies: 16
Views: 3,201
Posted By Matt Kearse
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...
Forum: Bioinformatics 02-26-2015, 12:58 PM
Replies: 18
Views: 5,948
Posted By Matt Kearse
If prior to import you give the FASTQ files names...

If prior to import you give the FASTQ files names that match their sample ID then their file name becomes the effective sample ID. Paired files should have an suffix (e.g 1 or 2) which will get...
Forum: Bioinformatics 02-25-2015, 01:03 PM
Replies: 18
Views: 5,948
Posted By Matt Kearse
Unfortunately no, there isn't a Geneious command...

Unfortunately no, there isn't a Geneious command line interface. You can align or variant call in bulk by selecting all the data sets and choosing the options once.

Or if that's not sufficient...
Forum: Bioinformatics 02-24-2015, 09:32 PM
Replies: 18
Views: 5,948
Posted By Matt Kearse
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...
Forum: Bioinformatics 02-18-2015, 11:21 AM
Replies: 18
Views: 5,948
Posted By Matt Kearse
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...
Forum: Bioinformatics 12-15-2014, 02:14 PM
Replies: 13
Views: 3,411
Posted By Matt Kearse
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...
Forum: Bioinformatics 11-18-2014, 03:24 PM
Replies: 18
Views: 6,413
Posted By Matt Kearse
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...
Forum: Bioinformatics 11-18-2014, 01:16 PM
Replies: 6
Views: 2,029
Posted By Matt Kearse
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...
Forum: Bioinformatics 07-24-2014, 12:05 AM
Replies: 3
Views: 1,868
Posted By Matt Kearse
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...
Forum: Bioinformatics 07-22-2014, 03:31 PM
Replies: 9
Views: 1,578
Posted By Matt Kearse
Geneious (which is commercial software) has nice...

Geneious (which is commercial software) has nice coverage visualization. You can also run the high/low coverage finder on each sample to annotate regions of high/low coverage. Then run the compare...
Forum: Bioinformatics 07-22-2014, 03:15 PM
Replies: 10
Views: 1,509
Posted By Matt Kearse
I'm a little late to this discussion since you've...

I'm a little late to this discussion since you've written what you need already. But since your solution isn't publicly available yet I'll point out that Geneious (which is commercial software) has...
Forum: Bioinformatics 07-10-2014, 12:52 PM
Replies: 12
Views: 2,445
Posted By Matt Kearse
Most likely the problem is the excessive level...

Most likely the problem is the excessive level coverage you've got. Most de novo assemblers (Geneious included) won't work well with that level of coverage. The reason is that the same random...
Forum: Bioinformatics 07-09-2014, 03:52 PM
Replies: 12
Views: 2,445
Posted By Matt Kearse
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...
Forum: Bioinformatics 05-08-2014, 01:20 PM
Replies: 24
Views: 15,252
Posted By Matt Kearse
It varies greatly between different cells, but I...

It varies greatly between different cells, but I think on average there are around 200 mitochondria per cell so you usually get a much higher level of mitochondrial coverage in a WGS data set...
Forum: Bioinformatics 05-08-2014, 12:01 AM
Replies: 24
Views: 15,252
Posted By Matt Kearse
No, I just used a whole genome data set without...

No, I just used a whole genome data set without any sort of filtering for mitochondria.
Forum: Bioinformatics 05-06-2014, 01:55 PM
Replies: 24
Views: 15,252
Posted By Matt Kearse
It's always good to have more than one way to do...

It's always good to have more than one way to do something to add confidence that your results are correct.

So for a completely different approach to MITObim, why not just de novo assemble your...
Forum: Bioinformatics 04-29-2014, 12:54 PM
Replies: 5
Views: 3,173
Posted By Matt Kearse
The free (unlicensed) version of Geneious can do...

The free (unlicensed) version of Geneious can do what you want. It also has an option to fill the consensus with either the reference sequence bases or Ns when either the coverage or quality of the...
Forum: Vendor Forum 03-13-2014, 12:31 PM
Replies: 2
Views: 2,292
Posted By Matt Kearse
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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