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Forum: Oxford Nanopore 05-12-2017, 05:02 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
@Brian Agreed on everything except You...

@Brian Agreed on everything except

You cannot map short reads containing only repetitive sequence to a long read spanning the repetitive region, can you? If you could, you would be able to map the...
Forum: Illumina/Solexa 05-12-2017, 04:22 AM
Replies: 12
Views: 1,228
Posted By WhatsOEver
Sorry for being stupid, but I still don't get it...

Sorry for being stupid, but I still don't get it ;)
We currently only have the MiSeq (other sequencing is outsourced), but we also have a back-end infrastructure processing the data offline....
Forum: Illumina/Solexa 05-12-2017, 03:53 AM
Replies: 12
Views: 1,228
Posted By WhatsOEver
And what is the advantage of doing so? I thought...

And what is the advantage of doing so? I thought "GenerateFastq" is the smallest, possible workflow I can use for a run? In that workflow fastqs are generated by applying bcl2fastq internally after...
Forum: Illumina/Solexa 05-11-2017, 11:38 PM
Replies: 12
Views: 1,228
Posted By WhatsOEver
But this is not the amount of data that normally...

But this is not the amount of data that normally needs to be send over the network, is it? I mean, you will only need all the other stuff (bcl, pics, etc.) if your data looks somehow weird. If the...
Forum: Illumina/Solexa 05-11-2017, 11:33 PM
Replies: 3
Views: 1,595
Posted By WhatsOEver
Do you need the fluidigm seq primer for anything...

Do you need the fluidigm seq primer for anything in the downstream processing? If not, I would suggest to run 10-20 dark cycles (depends if the primer seq is really at the start of every fragment) in...
Forum: Oxford Nanopore 05-11-2017, 05:59 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
According to the information we got from the ONT...

According to the information we got from the ONT developers it is not possible. And even if it would be, you will end up with 1X (or 2X for diploid...) only with no possibility to do error correction...
Forum: Oxford Nanopore 05-11-2017, 12:39 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
That would be great! Thanks! I'll have a look at...

That would be great! Thanks! I'll have a look at the RepliG generated worm data in the meantime.
Forum: Oxford Nanopore 05-10-2017, 11:29 PM
Replies: 44
Views: 7,652
Posted By WhatsOEver
How does this fit together? Could you tell us...

How does this fit together?
Could you tell us where you got this information from?
I would especially be interested in seeing some real data from this machine.
Forum: Oxford Nanopore 05-10-2017, 11:24 PM
Replies: 44
Views: 7,652
Posted By WhatsOEver
Is this human data? Could you share the raw data...

Is this human data? Could you share the raw data behind this? This might be an interesting region to evaluate our aims but I would need to check whether we are able to target this region with our...
Forum: Illumina/Solexa 05-10-2017, 11:02 PM
Replies: 12
Views: 1,228
Posted By WhatsOEver
Just out of curiosity: How do you get that amount...

Just out of curiosity: How do you get that amount of data per day? Our MiSeq requires 2.5 days to complete a 2x300bp run and shorter libraries do not produce that amount of data?!
Forum: Bioinformatics 05-10-2017, 10:56 PM
Replies: 3
Views: 688
Posted By WhatsOEver
[original post deleted because I misunderstood...

[original post deleted because I misunderstood the question]

gingers answer below is correct. You can simply confirm this by swapping R1 and R2 reads.
Forum: Oxford Nanopore 05-10-2017, 12:29 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
I will. And yes, it was for me indeed a very...

I will. And yes, it was for me indeed a very interesting and helpful discussion - thanks a lot to all participators!



Yepp, in the end its "accuracy vs cost". Pacbio with higher accuracy but...
Forum: Oxford Nanopore 05-10-2017, 12:15 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
Although this becomes a little off-topic now,...

Although this becomes a little off-topic now, what do you think in this context of the genia sequencer which (more or less) specifically addresses the difficulties in distinguishing similar signals...
Forum: Pacific Biosciences 05-09-2017, 11:49 PM
Replies: 5
Views: 2,655
Posted By WhatsOEver
Thanks a lot for your input @Bukowski. Could you...

Thanks a lot for your input @Bukowski. Could you just very briefly elaborate what "much higher" means here - should we expect 1k? 2k? More?
Forum: Oxford Nanopore 05-09-2017, 11:44 PM
Replies: 44
Views: 7,652
Posted By WhatsOEver
Its actually the variant calling for minimal cost...

Its actually the variant calling for minimal cost on whole genome level which is the critical part for me ;) I'm totally fine with our existing Illumina-Agilent-WES variant calling pipeline.
Forum: Oxford Nanopore 05-09-2017, 11:37 PM
Replies: 44
Views: 7,652
Posted By WhatsOEver
mhh, the discussion about ONT vs others seems to...

mhh, the discussion about ONT vs others seems to me a little like apple vs samsung: Either you hate it or you love it :D



Can't be, because this would imply that you already know that the...
Forum: Oxford Nanopore 05-08-2017, 02:25 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
Thanks for the info @gringer esp on pricing and...

Thanks for the info @gringer esp on pricing and output.
I would be grateful if you could further comment on the following:



Sorry, but based on the data I have seen (which is the NA12878 Human...
Forum: Bioinformatics 05-04-2017, 11:14 PM
Replies: 2
Views: 742
Posted By WhatsOEver
Why do you expect the genomes to have the exact...

Why do you expect the genomes to have the exact same sizes? "Closest" sequenced homolog can still be far far away. I would say you go for more meaningful assembly quality assessment criteria....
Forum: Oxford Nanopore 05-04-2017, 05:30 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
Thanks @nucacidhunter for your input. I also...

Thanks @nucacidhunter for your input.

I also thought that the length of our DNA fragments would be a major limitation, but actually heard that it probably isn't. This is because it has no...
Forum: Oxford Nanopore 05-04-2017, 02:00 AM
Replies: 44
Views: 7,652
Posted By WhatsOEver
ONT promethion for single cell human WGS?

Hi @all,
we are currently struggling with pros/cons of buying a PB sequel vs ONT Promethion for our analyses (human de novo single celll WGS). Ideally we are looking for something with which we can...
Forum: Pacific Biosciences 05-04-2017, 01:53 AM
Replies: 5
Views: 2,655
Posted By WhatsOEver
Pacbio sequel for single cell human WGS?

Hi @all,
we are currently struggling with pros/cons of buying a PB sequel vs ONT Promethion for our analyses (human de novo single celll WGS). Ideally we are looking for something with which we can...
Forum: Illumina/Solexa 04-25-2017, 05:26 AM
Replies: 2
Views: 722
Posted By WhatsOEver
1) bacteria often have a higher GC-content than...

1) bacteria often have a higher GC-content than eukaryots, so this might be a starting point
2) You could filter your dataset for the known symbionts (which genomes are available, at least acc to a...
Forum: Bioinformatics 04-11-2017, 10:16 PM
Replies: 307
Views: 84,105
Posted By WhatsOEver
Is the command you posted, when you got the error...

Is the command you posted, when you got the error the first time copy/paste from your terminal? In that case you simply made the mistake to only load the reverse reads ;)
That may also fit to the...
Forum: Bioinformatics 01-23-2017, 12:49 AM
Replies: 5
Views: 1,292
Posted By WhatsOEver
Need help with NGS hardware upgrade

Hi there,
I know this question comes up every now and then and is eventually hard to answer, but we have no sysadmin at hand with enough NGS experience and are in need to spend some money :D

We...
Forum: Bioinformatics 01-23-2017, 12:06 AM
Replies: 2
Views: 967
Posted By WhatsOEver
Looks like the jar was somehow wrongly build ...

Looks like the jar was somehow wrongly build
You should contact the authors
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