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Forum: Helicos / Direct Genomics 03-29-2013, 06:57 AM
Replies: 2
Views: 19,974
Posted By Calico
Anyone has Helicos' software?

Does anyone in the forum still have the source tarball for the HeliSphere software? Their website that hosted the software seems to ultimately have shut down. I tried searching for it online, but...
Forum: Bioinformatics 09-26-2012, 11:25 AM
Replies: 5
Views: 16,999
Posted By Calico
vivek_: Thanks, that worked quite beautifully. I...

vivek_: Thanks, that worked quite beautifully. I would never have expected the solution to be that trivial.

maubp: Yes, Biopython should work but it's not too easy to install NumPy and SciPy...
Forum: Bioinformatics 09-26-2012, 07:29 AM
Replies: 5
Views: 16,999
Posted By Calico
Combine two FASTA files

I have a couple of fasta files I want to combine, two and two. They're >1 GB so reading them in R is too time consuming. I'm running a Mac on which I can't get Biopython to work and I don't find any...
Forum: Helicos / Direct Genomics 05-25-2010, 11:02 AM
Replies: 19
Views: 37,312
Posted By Calico
It's a little bit sad to see, and strange since...

It's a little bit sad to see, and strange since they are one NGS company that actually has a machine on the market. What do you think is the reason for their demise? One thing I have noticed is the...
Forum: Bioinformatics 04-26-2010, 01:57 PM
Replies: 34
Views: 5,861
Posted By Calico
By the way, is the R environment not used in the...

By the way, is the R environment not used in the HTS community anymore?
Forum: Bioinformatics 04-21-2010, 05:20 AM
Replies: 34
Views: 5,861
Posted By Calico
I was hoping for a uniform answer. This leaves me...

I was hoping for a uniform answer. This leaves me with some thinking to do.

Thanks for the input.
Forum: Bioinformatics 04-20-2010, 07:09 AM
Replies: 34
Views: 5,861
Posted By Calico
Preferred languages to work in?

Hello everybody,

My rather limited bioinfromatics skills come from having done some microarray data analysis in R (following a template code) and some minor coursework. So, I consider myself quite...
Forum: Bioinformatics 04-14-2010, 01:19 PM
Replies: 36
Views: 21,696
Posted By Calico
Not yet, but I am about to subject some samples...

Not yet, but I am about to subject some samples to Helicos sequencing.
Forum: Bioinformatics 04-14-2010, 10:23 AM
Replies: 36
Views: 21,696
Posted By Calico
Is there any way that Galaxy can be used to...

Is there any way that Galaxy can be used to analyze data from a Helicos machine?
Forum: Introductions 02-02-2010, 06:52 AM
Replies: 4
Views: 1,927
Posted By Calico
I am interested in this as well but I do not find...

I am interested in this as well but I do not find most reviews and papers I have read helpful as for learning. Does anyone know any tutorial that really explains the procedures in detail?
Forum: Helicos / Direct Genomics 01-26-2010, 07:14 AM
Replies: 7
Views: 8,608
Posted By Calico
And that would be the case for Helicos as well? ...

And that would be the case for Helicos as well?
Are they imaged sequentially or all simultaneously (in that case, all ties of one channel or of one flow cell at the same time)?
Forum: Helicos / Direct Genomics 01-26-2010, 06:58 AM
Replies: 7
Views: 8,608
Posted By Calico
Allright, that photo at least clarifies why they...

Allright, that photo at least clarifies why they call them channels (i.e. they are channels). Though, now I am uncertain what the picture I posted is - a whole flow cell or a segment of a single...
Forum: Helicos / Direct Genomics 01-25-2010, 07:09 PM
Replies: 7
Views: 8,608
Posted By Calico
Flow cell/channel terminology

Hello all,

I am a little bit perplexed of the exact mening of the term 'channel' as it is used by Helicos. So, I understand that there machine has two flow cells - in one the synthesis reaction...
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