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Forum: Oxford Nanopore 10-19-2018, 04:43 PM
Replies: 0
Views: 353
Posted By gringer
Flongle flow cells - now shipping

Oxford Nanopore Technologies have started shipping Flongle adapters and flow cells to customers. These are disposable flow cells using fewer pores and a cheaper design ($5000 USD for 48 flow cells)....
Forum: Oxford Nanopore 09-28-2018, 04:42 AM
Replies: 14
Views: 4,383
Posted By gringer
You need a solid-state disk as the main disk for...

You need a solid-state disk as the main disk for the computer (I'm not quite sure what "HHD" means). Other things should be fine.
Forum: Sample Prep / Library Generation 09-04-2018, 04:21 AM
Replies: 4
Views: 903
Posted By gringer
OpenTrons

If you want cheap, there's the OpenTrons OT-2 (http://opentrons.com/ot-2). The basic system is $3500 USD, with additional modules ordered separately:


single channel pipette $500
8-channel...
Forum: Bioinformatics 09-04-2018, 03:43 AM
Replies: 2
Views: 553
Posted By gringer
Use supertranscripts as your reference genome: ...

Use supertranscripts as your reference genome:

https://github.com/Oshlack/Lace/wiki

https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts
Forum: Bioinformatics 08-05-2018, 06:53 AM
Replies: 1
Views: 696
Posted By gringer
What is the question you are trying to answer by...

What is the question you are trying to answer by doing this mapping?
Forum: Bioinformatics 08-05-2018, 06:32 AM
Replies: 97
Views: 22,343
Posted By gringer
Wow! Joined in 2014, only one post, and you chose...

Wow! Joined in 2014, only one post, and you chose to make your first post something about mutant clouds in response to a 3-year old post of mine from the first page of this thread. I'm not sure if I...
Forum: Oxford Nanopore 05-30-2018, 06:29 AM
Replies: 1
Views: 1,032
Posted By gringer
Clive Brown's Technology Talk from London Calling 2018

For the last 4 years I've attended Oxford Nanopore Technologies' yearly London Calling conference. One of the interesting bits of this conference is the talk from Clive Brown about what's happening...
Forum: Bioinformatics 05-28-2018, 06:20 AM
Replies: 1
Views: 457
Posted By gringer
That should be fine. Inchworm does a kmer-based...

That should be fine. Inchworm does a kmer-based assembly, so as long as the reads are longer than the size of the kmers, it should be okay.

However, it'd be a good idea to do adapter and end...
Forum: Bioinformatics 04-22-2018, 05:31 AM
Replies: 2
Views: 390
Posted By gringer
If you don't care about accuracy, just...

If you don't care about accuracy, just concatenate all the fasta sequences into a single large sequence....

More seriously, you're probably not going to get any better continuity from your data...
Forum: Bioinformatics 04-22-2018, 05:25 AM
Replies: 13
Views: 1,592
Posted By gringer
That's not the only reason. Sigma also has...

That's not the only reason. Sigma also has region-specific pricing. Without logging in, I choose the location when I first visit the site (presumably stored as a cookie for subsequent visits), and...
Forum: Bioinformatics 04-22-2018, 04:00 AM
Replies: 13
Views: 1,592
Posted By gringer
You won't be able to get a good de-novo assembly...

You won't be able to get a good de-novo assembly from Illumina data alone, and longer SBS reads won't fix that. Consider things like 28S rRNA gene regions, where kilobase-length regions are repeated...
Forum: Bioinformatics 04-20-2018, 05:25 PM
Replies: 13
Views: 1,592
Posted By gringer
As far as I know, ONT is the only sequencing...

As far as I know, ONT is the only sequencing machine supplier that publishes all their prices on their store website; you can have a look and see for yourself!

At the moment marginal cost per base...
Forum: Bioinformatics 04-17-2018, 05:37 PM
Replies: 13
Views: 1,592
Posted By gringer
If you want cheap,...

If you want cheap, [MinION](https://store.nanoporetech.com/basic.html) is always available (starter discount is $1000 for two flow cells and a rapid kit). The consensus assemblies are less accurate...
Forum: Metagenomics 04-17-2018, 05:32 PM
Replies: 1
Views: 894
Posted By gringer
Unlikely. Sanger sequencing doesn't really work...

Unlikely. Sanger sequencing doesn't really work with variants at a frequency below about 20%, and any INDEL variation in the community is going to mess up the sequencing quite a lot.
Forum: General 04-17-2018, 05:12 PM
Replies: 2
Views: 1,316
Posted By gringer
I'd recommend doing an analysis on the unmapped...

I'd recommend doing an analysis on the unmapped reads to make sure that they are not hitting something other than your intended target. With a tumour sample it's unlikely to be a contamination issue,...
Forum: Bioinformatics 04-17-2018, 05:06 PM
Replies: 1
Views: 327
Posted By gringer
My usual approach is to do the mapping...

My usual approach is to do the mapping separately, and do variant calling in parallel with samtools mpileup in multi-BAM mode (i.e. using more than one BAM file on the command line). This increases...
Forum: Bioinformatics 02-19-2018, 10:31 AM
Replies: 3
Views: 694
Posted By gringer
Something else to try: get rid of reads that have...

Something else to try: get rid of reads that have '.' in their sequence:

http://seqanswers.com/forums/showthread.php?t=6297
Forum: Bioinformatics 02-18-2018, 03:33 PM
Replies: 3
Views: 694
Posted By gringer
I expect that you should be putting csfastq files...

I expect that you should be putting csfastq files into bowtie, rather than csfasta + qual.

But you'd be a lot better off leaving SOLiD data alone. Replicate the experiment using full-length cDNA...
Forum: Oxford Nanopore 02-04-2018, 11:36 PM
Replies: 5
Views: 2,139
Posted By gringer
I can tell you what I use, but it's unlikely to...

I can tell you what I use, but it's unlikely to be what other people prefer, because there's a lot of manual computational legwork involved.

De-novo Assembly -- Canu...
Forum: Bioinformatics 02-03-2018, 12:57 PM
Replies: 4
Views: 1,219
Posted By gringer
My probably-biased point of view (as a...

My probably-biased point of view (as a bioinformatician) is that even with the original CLC prices, a company would get more benefit out of hiring a dedicated bioinformatician than paying for CLC.
...
Forum: Oxford Nanopore 02-03-2018, 12:52 PM
Replies: 5
Views: 2,139
Posted By gringer
Both the command-line program ONT provides for...

Both the command-line program ONT provides for basecalling (Albacore) and the GUI Client that does sequencing and optionally basecalling (MinKNOW) can now output fastq files directly, no need to...
Forum: Oxford Nanopore 01-30-2018, 11:09 AM
Replies: 4
Views: 3,356
Posted By gringer
The costs you have stated are per sequencing run,...

The costs you have stated are per sequencing run, not per sample (i.e. $100 per run + $56 per run), so divide those numbers by six; please re-read the post that you replied to.

If bacterial genome...
Forum: Pacific Biosciences 12-18-2017, 01:03 AM
Replies: 14
Views: 4,119
Posted By gringer
As fas as I know, canu also doesn't use quality...

As fas as I know, canu also doesn't use quality scores for assembly. By default it does its own error correction based on an all-vs-all read mapping, and produces corrected FASTA files (i.e. without...
Forum: Oxford Nanopore 12-18-2017, 12:40 AM
Replies: 4
Views: 3,356
Posted By gringer
Nanopore costs are all available on the nanopore...

Nanopore costs are all available on the nanopore store website (https://store.nanoporetech.com/kits-218.html). Here are some demonstrative figures:


Flow cells at their most expensive are $900...
Forum: Oxford Nanopore 11-03-2017, 11:49 AM
Replies: 4
Views: 2,797
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.
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