SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.05 seconds.
Search: Posts Made By: gringer
Forum: Oxford Nanopore 11-03-2017, 11:49 AM
Replies: 4
Views: 796
Posted By gringer
Nanopolish also now includes methylation in its...

Nanopolish also now includes methylation in its correction model, which (according to Ryan Wick) has brought the nanopore-only consensus accuracy up to q30 for a bacterial genome.
Forum: RNA Sequencing 10-23-2017, 01:56 AM
Replies: 2
Views: 604
Posted By gringer
It is a type of technical replicate, but will...

It is a type of technical replicate, but will have some degree of biological variation from the different samples. Usually "technical replicate" refers to an additional sequencing library prepared...
Forum: Bioinformatics 10-23-2017, 01:47 AM
Replies: 2
Views: 378
Posted By gringer
Should the refcount be the sum of the count of...

Should the refcount be the sum of the count of the two assemblies (i.e. 60528, not 28905)?
Forum: Illumina/Solexa 10-18-2017, 11:59 AM
Replies: 26
Views: 2,203
Posted By gringer
I was told by an Illumina rep at Queenstown...

I was told by an Illumina rep at Queenstown Research week about a month ago that NovaSeq run cost would be similar to HiSeq, but produce about double the output.
Forum: Oxford Nanopore 09-25-2017, 03:28 PM
Replies: 4
Views: 796
Posted By gringer
The 'ont2d' flag sets up BWA parameters to work...

The 'ont2d' flag sets up BWA parameters to work for ONT data. It was named at a time when 2D data was similar accuracy to what 1D data is at the moment. You should be fine using Albacore 2.0-called...
Forum: General 08-25-2017, 05:09 PM
Replies: 3
Views: 609
Posted By gringer
Experimental design: not choosing appropriate...

Experimental design: not choosing appropriate controls, too few biological replicates, or doing sequencing on the wrong cell population (e.g. whole-blood RNASeq for an obesity study).
Forum: Bioinformatics 08-23-2017, 04:30 AM
Replies: 4
Views: 573
Posted By gringer
Samtools mpileup has its own INDEL correction,...

Samtools mpileup has its own INDEL correction, which may be influencing the results that you're seeing. You could try skipping this (option `-IŽ) and seeing if it changes the results.
Forum: Oxford Nanopore 08-20-2017, 06:42 PM
Replies: 5
Views: 1,181
Posted By gringer
My recommendation would be to get the basic...

My recommendation would be to get the basic starter pack and muddle your way through the sequencing process yourself (with help from the community forums). You'll fail more, learn more, and learn...
Forum: Oxford Nanopore 08-20-2017, 06:49 AM
Replies: 5
Views: 1,181
Posted By gringer
You can't get two basic, unless you have two...

You can't get two basic, unless you have two labs. The basic discount is one-off. To get a similar discount after the first flow cells, you need to purchase 48 of them over the course of a year.
...
Forum: SOLiD 08-06-2017, 09:44 PM
Replies: 4
Views: 3,222
Posted By gringer
Anything that gets you quicker to re-analysing...

Anything that gets you quicker to re-analysing your target sample with a non-SOLiD system. You shouldn't be mapping SOLiD reads at all, especially not 35bp ones; interpreting the results is just too...
Forum: Oxford Nanopore 08-02-2017, 04:34 AM
Replies: 11
Views: 1,033
Posted By gringer
If you find a functional gene in one human...

If you find a functional gene in one human population, it is highly likely that that gene exists in all human populations. Perhaps you could post your question as a separate thread; it doesn't seem...
Forum: Oxford Nanopore 08-02-2017, 12:53 AM
Replies: 11
Views: 1,033
Posted By gringer
Er... don't use fastx-toolkit for nanopore files....

Er... don't use fastx-toolkit for nanopore files. It was designed more than a few years ago, and is probably not coded to be able to handle lines with tens of thousands of bases.

And before the...
Forum: The Pipeline 07-24-2017, 06:14 AM
Replies: 1
Views: 1,205
Posted By gringer
Heteroplasmy can't exceed 50% unless the analysis...

Heteroplasmy can't exceed 50% unless the analysis is done at a haplotype level (i.e. considering multiple variants). For a single bimorphic variant, a heteroplasmy of greater than 50% would imply...
Forum: Pacific Biosciences 06-22-2017, 06:26 AM
Replies: 9
Views: 810
Posted By gringer
Nanopore isn't able to generate a full-length...

Nanopore isn't able to generate a full-length read per bacterial genome yet, but Nick Loman has had one run where he found 7 reads that covered the whole E. coli genome.

For single isolates,...
Forum: Pacific Biosciences 06-22-2017, 01:10 AM
Replies: 9
Views: 810
Posted By gringer
For comparison, the MinION consumable costs (in...

For comparison, the MinION consumable costs (in USD) are available on the ONT website (https://store.nanoporetech.com). Here are some examples:

Initial [capital] cost: $1000 (includes 2x flow...
Forum: Bioinformatics 06-22-2017, 12:26 AM
Replies: 2
Views: 1,612
Posted By gringer
How does it deal with artefacts caused by index...

How does it deal with artefacts caused by index swapping (or similar)?
Forum: Pacific Biosciences 06-15-2017, 05:35 PM
Replies: 62
Views: 17,319
Posted By gringer
From what I've been told, really good PacBio runs...

From what I've been told, really good PacBio runs produce about 10Gb of sequence data. I would expect that PacBio will produce less raw data than nanopore for the same sequence output, so I expect...
Forum: General 06-04-2017, 08:01 PM
Replies: 4
Views: 692
Posted By gringer
LAST and GraphMap should also work.

LAST and GraphMap should also work.
Forum: Oxford Nanopore 06-01-2017, 07:46 AM
Replies: 11
Views: 2,534
Posted By gringer
Thanks. I'll try to remember to check the website...

Thanks. I'll try to remember to check the website before making statements like that again.

https://store.nanoporetech.com/minion/sets
Forum: Oxford Nanopore 05-30-2017, 03:41 PM
Replies: 11
Views: 2,534
Posted By gringer
The phage experiment is a short run; you can use...

The phage experiment is a short run; you can use the same flow cell for another experiment later on. I'm not sure if the starter pack includes a wash kit, but you can order one from ONT (currently...
Forum: Bioinformatics 05-29-2017, 01:19 PM
Replies: 3
Views: 513
Posted By gringer
By plotting the rank (assuming you have actually...

By plotting the rank (assuming you have actually plotted the rank), you've removed any parametric factors from the plot. If you're doing a PCA on the rank then this would be fine, but I suspect your...
Forum: Bioinformatics 05-26-2017, 09:12 PM
Replies: 3
Views: 513
Posted By gringer
I've had the best results from PCAs based on...

I've had the best results from PCAs based on DESeq2 results when I used the VST and did an additional correction for transcript length (i.e. divide the by the longest transcript per gene in kb). This...
Forum: Sample Prep / Library Generation 05-26-2017, 08:49 PM
Replies: 9
Views: 1,344
Posted By gringer
And even fluorimetry can get it wrong. If there's...

And even fluorimetry can get it wrong. If there's a huge amount of RNA in the sample (e.g. 100x as much as DNA), or contamination with a fluorescent substance (e.g. coffee), it can affect the result....
Forum: Bioinformatics 05-20-2017, 02:01 PM
Replies: 12
Views: 852
Posted By gringer
Sorry, I am in a very strange work situation as a...

Sorry, I am in a very strange work situation as a freelance bioinformatician. It sounded like your arrangement was similar to my own, because you mentioned your contract being "over". The majority of...
Forum: Bioinformatics 05-19-2017, 09:55 PM
Replies: 12
Views: 852
Posted By gringer
I've found as a contractor that its better to be...

I've found as a contractor that its better to be surprised/pleased when my name is added to a paper, than annoyed when it's excluded. I do enough different projects that it's not worth the effort (or...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 07:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO