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Forum: Bioinformatics 09-25-2018, 10:47 AM
Replies: 657
Views: 137,838
Posted By SNPsaurus
Have you trimmed adapters away from the reads...

Have you trimmed adapters away from the reads (short fragments will create reads that are part genomic and part adapter and may not map). You could use the related BBmap tool sendsketch to get a...
Forum: General 09-12-2018, 09:03 PM
Replies: 1
Views: 924
Posted By SNPsaurus
RNA-Seq may use 10-30 million reads in an...

RNA-Seq may use 10-30 million reads in an experiment for expression profiling. SAGE would collect 10-50 thousand SAGE tags or so for a profile?
Forum: Bioinformatics 08-24-2018, 12:47 PM
Replies: 10
Views: 697
Posted By SNPsaurus
I'm not sure what is being measured by the...

I'm not sure what is being measured by the duplication level...I thought you were marking PCR duplicates.

If you have 1 million EcoRI sites, then I'd pick the best 15 samples (high alignment rate,...
Forum: Bioinformatics 08-24-2018, 12:09 PM
Replies: 10
Views: 697
Posted By SNPsaurus
You can't think about coverage that way with...

You can't think about coverage that way with RAD-Seq. You know that coverage will be zero across most of the genome, but then you will get high read depth at the RAD loci at the EcoRI sites. So I...
Forum: Bioinformatics 08-24-2018, 11:40 AM
Replies: 10
Views: 697
Posted By SNPsaurus
I think the problem is that you are sampling...

I think the problem is that you are sampling 500,000 sites which turns into 1 million RAD tags possible (each cut site has two tags that are sequenced) with an average of 500,000 reads per sample. So...
Forum: Bioinformatics 08-24-2018, 10:44 AM
Replies: 10
Views: 697
Posted By SNPsaurus
Was this regular RAD-Seq or ddRAD? There are...

Was this regular RAD-Seq or ddRAD? There are probably 500,000 EcoRI sites in a 2 Gb genome, so if you had 48 samples and 25 million reads even with perfect data you would get a read per site unless...
Forum: Bioinformatics 08-23-2018, 10:52 PM
Replies: 10
Views: 697
Posted By SNPsaurus
You have to be a little careful thinking about...

You have to be a little careful thinking about read coverage with RAD data...after all, it is meant to sample the genome at a small number of loci. So a "good" RAD sample might get 20X read depth at...
Forum: Genomic Resequencing 08-16-2018, 09:55 PM
Replies: 2
Views: 1,088
Posted By SNPsaurus
I haven't seen that error before. Were both bam...

I haven't seen that error before. Were both bam files sorted? Can you make a vcf file for each sample?
Forum: Bioinformatics 07-25-2018, 04:03 PM
Replies: 2
Views: 482
Posted By SNPsaurus
A phylip file should have actual DNA sequence for...

A phylip file should have actual DNA sequence for each sample, shouldn't it?
http://scikit-bio.org/docs/0.2.3/generated/skbio.io.phylip.html
Forum: Pacific Biosciences 07-04-2018, 12:10 PM
Replies: 2
Views: 1,235
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, 10:16 AM
Replies: 0
Views: 794
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, 11:18 PM
Replies: 3
Views: 2,213
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, 01:39 PM
Replies: 2
Views: 364
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, 03:24 PM
Replies: 6
Views: 1,162
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, 03:13 PM
Replies: 7
Views: 1,073
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, 02:04 PM
Replies: 7
Views: 1,073
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, 07:46 PM
Replies: 0
Views: 1,002
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, 09:28 AM
Replies: 1
Views: 485
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, 04:21 PM
Replies: 7
Views: 1,200
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, 11:32 AM
Replies: 3
Views: 968
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, 04:26 PM
Replies: 657
Views: 137,838
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, 12:26 PM
Replies: 657
Views: 137,838
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, 10:41 AM
Replies: 657
Views: 137,838
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, 09:29 PM
Replies: 7
Views: 1,884
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, 09:17 PM
Replies: 6
Views: 1,095
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/
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