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Search: Posts Made By: Bukowski
Forum: Bioinformatics 08-20-2018, 03:59 AM
Replies: 4
Views: 461
Posted By Bukowski
Are you running under a job scheduler? I just...

Are you running under a job scheduler? I just tried to run the tests, but merman doesn't seem to compile under g++ 5.5.0 - and in fact there's an open issue on that repo that's 3.5 years old, which...
Forum: Bioinformatics 08-20-2018, 03:21 AM
Replies: 4
Views: 461
Posted By Bukowski
Your file name is too long. Shorten it? Where is...

Your file name is too long. Shorten it? Where is that underscore based hell being derived from? If it's coming from the temporary data directory creation try specify a tempdir at execution
Forum: Illumina/Solexa 07-25-2018, 03:13 AM
Replies: 14
Views: 775
Posted By Bukowski
What's your %PhiX?

What's your %PhiX?
Forum: RNA Sequencing 07-05-2018, 03:24 AM
Replies: 2
Views: 659
Posted By Bukowski
What do you mean by 'opposite'?

What do you mean by 'opposite'?
Forum: Ion Torrent 06-15-2018, 02:10 PM
Replies: 3
Views: 983
Posted By Bukowski
"Accuracy Accurate down to 384-well plates" ...

"Accuracy Accurate down to 384-well plates"

This is a new measure of accuracy that I was previously unaware of.

Their only 'Sequencing Application' in their protocol library is for 16S. There...
Forum: Bioinformatics 06-14-2018, 05:28 AM
Replies: 3
Views: 442
Posted By Bukowski
Some minION sequencing? There's nothing...

Some minION sequencing?

There's nothing wrong with that number of contigs from a 2x250 MiSeq run.
Forum: Bioinformatics 06-14-2018, 01:20 AM
Replies: 3
Views: 442
Posted By Bukowski
Yes, because it acts as an optimiser for Spades.....

Yes, because it acts as an optimiser for Spades.. which is perfectly happy with just short read data.
Forum: Bioinformatics 03-29-2018, 03:20 AM
Replies: 3
Views: 930
Posted By Bukowski
Well - you try pipetting so accurately that you...

Well - you try pipetting so accurately that you can manage better... ;)

Quantification isn't exact. Dilution isn't exact. Pooling isn't exact.
Forum: Bioinformatics 03-23-2018, 04:31 AM
Replies: 5
Views: 810
Posted By Bukowski
Use rsync?

Use rsync?
Forum: Illumina/Solexa 02-28-2018, 11:55 AM
Replies: 2
Views: 873
Posted By Bukowski
I don't really know what your application is, but...

I don't really know what your application is, but leaving yourself only 5 bp overlap for the reads at 2x75 doesn't sound like its the ideal strategy for flashing reads. How much fidelity do you need...
Forum: Bioinformatics 02-10-2018, 03:42 PM
Replies: 3
Views: 764
Posted By Bukowski
It's down. https://gitlab.com/ezlab/busco ...

It's down.

https://gitlab.com/ezlab/busco

You can find links to the code and datasets there.
Forum: Bioinformatics 01-22-2018, 12:58 AM
Replies: 15
Views: 1,262
Posted By Bukowski
What was the goal of sequencing them in the first...

What was the goal of sequencing them in the first place? This might inform any potential answers...
Forum: Ion Torrent 01-17-2018, 03:58 AM
Replies: 5
Views: 1,910
Posted By Bukowski
'Deblur has not been evaluated with Ion Torrent':...

'Deblur has not been evaluated with Ion Torrent': https://forum.qiime2.org/t/deblur-p-trim-length-deactivation-failure/1880/5

DADA2 recommendations for Ion Torrent data:...
Forum: Illumina/Solexa 12-19-2017, 03:44 AM
Replies: 2
Views: 801
Posted By Bukowski
https://support.illumina.com/downloads/sequencing_...

https://support.illumina.com/downloads/sequencing_coverage_calculator.html
Forum: Bioinformatics 11-09-2017, 03:40 AM
Replies: 2
Views: 574
Posted By Bukowski
https://www.biostars.org/p/109425/

https://www.biostars.org/p/109425/
Forum: Academic/Non-Profit Jobs 10-12-2017, 07:58 AM
Replies: 0
Views: 402
Posted By Bukowski
Research Fellow in Microbial Genomics, Aberdeen - Sctoland

Posting on behalf of a colleague:

REF: SBS028R

We seek a highly motivated and interactive Microbial Genomicist to take a leading role in a Natural Environment Research Council-funded project...
Forum: Academic/Non-Profit Jobs 08-07-2017, 01:34 AM
Replies: 0
Views: 386
Posted By Bukowski
Genomics Pipeline Group Software Developer - Earlham Institute, Norwich UK

We currently have a job open in the Genomics Pipelines Group for a Software Developer. Please note this is not a bioinformatics post per se, but will work closely with bioinformaticians and others in...
Forum: Industry Jobs! 08-02-2017, 05:30 AM
Replies: 0
Views: 7,011
Posted By Bukowski
Bioinformatician/statistical genetcisist - Cytox Ltd (UK)

I'm not posting this on behalf of myself, but for a company I worked with on a project a couple of years ago who I'm prepared to vouch for in terms of how interesting I think the role might be for...
Forum: Bioinformatics 05-19-2017, 03:29 AM
Replies: 12
Views: 1,336
Posted By Bukowski
How's your lawsuit going? Question is...

How's your lawsuit going?

Question is rhetorical. I've met far more people who allege malpractice of this type in the industry, than seen malpractice of this type in the industry...
Forum: Pacific Biosciences 05-09-2017, 11:56 PM
Replies: 5
Views: 2,634
Posted By Bukowski
The Sequel consumables starter kit, which...

The Sequel consumables starter kit, which provides enough materials for 16 cells is 20k - admittedly this is not the cheapest way to buy consumables, but is closer to 1.25k/cell.
Forum: Pacific Biosciences 05-09-2017, 10:27 AM
Replies: 5
Views: 2,634
Posted By Bukowski
1) Accuracy of >99.999% - Yes this will be...

1) Accuracy of >99.999%

- Yes this will be consensus accuracy at depth.

2) Output of ~5Gb per SMRT cell / ~800 per SMRT cell run

- That's about what we're seeing. Without going too far...
Forum: Bioinformatics 04-07-2017, 04:00 AM
Replies: 3
Views: 686
Posted By Bukowski
http://biorxiv.org/content/early/2016/08/12/068809

http://biorxiv.org/content/early/2016/08/12/068809
Forum: Bioinformatics 03-31-2017, 11:09 AM
Replies: 10
Views: 1,827
Posted By Bukowski
You're looking at the wrong genome...

You're looking at the wrong genome build/annotation in IGV almost certainly.
Forum: Illumina/Solexa 03-23-2017, 01:50 AM
Replies: 29
Views: 6,109
Posted By Bukowski
So.. no this issue is not resolved. I have an...

So.. no this issue is not resolved. I have an email from Illumina today which I will summarise.

The issue is that there is a byproduct in their manufacturing process of fluorescent nucleotides....
Forum: Illumina/Solexa 03-02-2017, 08:29 AM
Replies: 8
Views: 1,653
Posted By Bukowski
That library prep is about as simple as it gets....

That library prep is about as simple as it gets. What you need is automation, not a different method.
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