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Forum: Pacific Biosciences 07-04-2018, 11:10 AM
Replies: 2
Views: 414
Posted By SNPsaurus
As nucacidhunter says, while there is worry that...

As nucacidhunter says, while there is worry that multi-copy plasmids will overwhelm a sample, in practice plasmids can be under-represented. In the below examples, the plasmids are part of the...
Forum: Vendor Forum 06-28-2018, 09:16 AM
Replies: 0
Views: 323
Posted By SNPsaurus
SNPsaurus offers Illumina bacterial genome sequencing service

SNPsaurus is now offering Illumina PE 150 sequencing of bacterial genomes: library prep, sequencing to 60X read depth, assembly, annotation, and alignment to a reference with variant...
Forum: Core Facilities 06-06-2018, 10:18 PM
Replies: 3
Views: 570
Posted By SNPsaurus
Most core facilities are subsidized by the...

Most core facilities are subsidized by the university and do not need to develop a full cost accounting for the operation of their equipment. They look at prevailing rates, charge something similar,...
Forum: Bioinformatics 05-09-2018, 12:39 PM
Replies: 2
Views: 252
Posted By SNPsaurus
vcftools does have a --thin option, and if you...

vcftools does have a --thin option, and if you set it to the maximum contig size then there will be only 1 SNP per contig (--thin 100000, for example).

It may select the first SNP in the contig,...
Forum: Illumina/Solexa 04-25-2018, 02:24 PM
Replies: 6
Views: 799
Posted By SNPsaurus
You should check out the Illumina free adapter...

You should check out the Illumina free adapter blocking kit that they recently released to mitigate the examp index hopping. You might still want to go dual unique, but just keep it in mind.
Forum: Illumina/Solexa 04-25-2018, 02:13 PM
Replies: 7
Views: 799
Posted By SNPsaurus
We got good results with both NextSeq and...

We got good results with both NextSeq and HiSeq4000 runs, so I think you are safe either way. Given the size of the genome, I'd want as much sequence information at each locus to help improve the...
Forum: Illumina/Solexa 04-25-2018, 01:04 PM
Replies: 7
Views: 799
Posted By SNPsaurus
I am very surprised that you see just 100k...

I am very surprised that you see just 100k fragments for a 6-cutter plus 4-cutter and a size selection of 150-550 bp. The 4-cutter will cut primarily every 150 bp - 350 bp, so your size selection...
Forum: Service Providers 04-15-2018, 06:46 PM
Replies: 0
Views: 575
Posted By SNPsaurus
Whole genome genotyping service

SNPsaurus is now offering whole genome genotyping. We can do complete genome sequencing at read depths appropriate for genotyping for species with small genomes at a similar price per sample as our...
Forum: Bioinformatics 04-09-2018, 08:28 AM
Replies: 1
Views: 423
Posted By SNPsaurus
I think it depends on the precise definition of...

I think it depends on the precise definition of depth you are using:
read depth-treat them all independently
fragment depth-count overlaps once
de-duplicated read depth-count overlaps once, and...
Forum: Service Providers 04-05-2018, 03:21 PM
Replies: 7
Views: 744
Posted By SNPsaurus
We're starting up a Illumina sequencing service...

We're starting up a Illumina sequencing service to complement our PacBio genome sequencing. We would do your 15 samples, starting from DNA (library prep, sequencing to 60X read depth with paired end...
Forum: Bioinformatics 03-29-2018, 10:32 AM
Replies: 3
Views: 864
Posted By SNPsaurus
Sure, fragmented DNA may make libraries that have...

Sure, fragmented DNA may make libraries that have a shorter fragment length. Unless you are precise in figuring out how many fragments are in your sample's library, the normalization will be off (and...
Forum: Bioinformatics 03-21-2018, 03:26 PM
Replies: 636
Views: 125,999
Posted By SNPsaurus
The reference in this case is a list of RAD loci...

The reference in this case is a list of RAD loci sequences, each at 150 bp. The reads are 150 bp and should match one of the RAD loci. Since there are no N (or degenerate nucleotides) in the...
Forum: Bioinformatics 03-21-2018, 11:26 AM
Replies: 636
Views: 125,999
Posted By SNPsaurus
I have a question about the bbmap summary output....

I have a question about the bbmap summary output. Here is an example:

Reads Used: 1061591 (151284618 bases)

Mapping: 15.250 seconds.
Reads/sec: 69611.57...
Forum: Bioinformatics 03-16-2018, 09:41 AM
Replies: 636
Views: 125,999
Posted By SNPsaurus
You might try the align2.BBMapPacBioSkimmer...

You might try the align2.BBMapPacBioSkimmer mapper with ambig=all and expectedsites= some high number. Not exactly what you were asking but I get dozens of hits with that.
Forum: Illumina/Solexa 03-01-2018, 08:29 PM
Replies: 7
Views: 1,765
Posted By SNPsaurus
We've had some issues with different WGA...

We've had some issues with different WGA libraries and Nextera in that WGA methods often create lots of ssDNA which will interfere with proper quantification and perhaps sop up transposomes.
Forum: Bioinformatics 02-26-2018, 08:17 PM
Replies: 6
Views: 839
Posted By SNPsaurus
We use the University of Oregon sequencing...

We use the University of Oregon sequencing facility, which has a PacBio Sequel, MiSeq and Hiseq4000. https://gc3f.uoregon.edu/
Forum: Bioinformatics 02-26-2018, 08:10 PM
Replies: 301
Views: 77,859
Posted By SNPsaurus
When you say you checked the header do you mean...

When you say you checked the header do you mean you looked at the the 364th and 365th read? What happens if you take some other random set of reads from the input and use that? Like
zcat...
Forum: Bioinformatics 02-19-2018, 07:34 PM
Replies: 2
Views: 430
Posted By SNPsaurus
Can you make a de novo reference in Stacks and...

Can you make a de novo reference in Stacks and blast the loci sequences to see what they are? As mastal says, it could be that your samples are heavily contaminated with some other species (like...
Forum: Bioinformatics 02-08-2018, 08:03 PM
Replies: 94
Views: 19,485
Posted By SNPsaurus
Do you need to use k=96? That is a large kmer...

Do you need to use k=96? That is a large kmer size and will increase memory demand. A metagenome plus sequence errors will create many 96-mers. What happens with the default k=31... does it run with...
Forum: Illumina/Solexa 01-03-2018, 09:17 AM
Replies: 13
Views: 1,983
Posted By SNPsaurus
I was trying to understand the niche of Firefly...

I was trying to understand the niche of Firefly from that tweet. 6M reads, length of 2x150, 16 hour runtime. That sounds very similar to a MiSeq micro run.
Forum: Pacific Biosciences 11-29-2017, 08:32 AM
Replies: 5
Views: 1,562
Posted By SNPsaurus
You could look at completeness by running Busco...

You could look at completeness by running Busco on it. http://busco.ezlab.org/
Forum: Vendor Forum 11-16-2017, 09:14 PM
Replies: 1
Views: 1,870
Posted By SNPsaurus
Here's a non-technical blog post showing how...

Here's a non-technical blog post showing how PacBio reads can power through a bacterial genome assembly even for a subpar sample with somewhat degraded DNA:...
Forum: Sample Prep / Library Generation 11-09-2017, 09:42 AM
Replies: 9
Views: 1,098
Posted By SNPsaurus
I'm curious what your goals are for the project....

I'm curious what your goals are for the project. There might be several million of each site in the genome (if it is 1 Gb). Even if you took the largest 5% of fragments, that could be several hundred...
Forum: Sample Prep / Library Generation 11-08-2017, 01:46 PM
Replies: 9
Views: 1,098
Posted By SNPsaurus
I was thinking about this some more, and I think...

I was thinking about this some more, and I think the use of two 4-cutters may be creating conditions that enrich for this sort of artifact.

What is your size selection range? Most people do ddRAD...
Forum: Sample Prep / Library Generation 11-08-2017, 09:47 AM
Replies: 9
Views: 1,098
Posted By SNPsaurus
Could you be getting chimeras of adapter - NlaIII...

Could you be getting chimeras of adapter - NlaIII - fragment 1 - MluCI - fragment 2 - MluCI - adapter?

You would see different sequences after the first MluCI for a given locus if so.

These are...
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