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Search: Posts Made By: Nomijill
Forum: Bioinformatics 01-19-2013, 04:27 AM
Replies: 37
Views: 6,389
Posted By Nomijill
As a taxpayer

I work for a commercial company, and our software is compared to Galaxy all the time, and we are glad that Galaxy and other publicly available tools are creating software. It drives us and other...
Forum: Introductions 04-01-2012, 08:17 PM
Replies: 1
Views: 630
Posted By Nomijill
Nice to meet you. I think you are going to find...

Nice to meet you. I think you are going to find this a very helpful site for both of your applications.
Forum: Bioinformatics 04-01-2012, 08:15 PM
Replies: 12
Views: 6,249
Posted By Nomijill
At CLC bio we have several tutorials...

At CLC bio we have several tutorials (http://www.clcbio.com/index.php?id=649http://) for RNASeq analysis. They are a great way for a beginner to understand the various steps required, and you will...
Forum: Bioinformatics 03-27-2012, 05:05 AM
Replies: 65
Views: 29,493
Posted By Nomijill
CLC bio Support

Please, whenever you have questions about the behavior of the CLC bio assemblers, contact [email protected] You may also be interested in trying the new version of the assembler, if you have not...
Forum: De novo discovery 02-22-2012, 03:25 PM
Replies: 26
Views: 25,696
Posted By Nomijill
Update on the CLC bio de novo assembler- It has...

Update on the CLC bio de novo assembler- It has scaffolding. It has the ability to control for bubble size, and it is faster than ever. I assemble 10 million paired end MiSeq reads in 15 minutes on...
Forum: Bioinformatics 10-15-2011, 01:10 PM
Replies: 11
Views: 1,849
Posted By Nomijill
Hi Kashliks, If you want to try the trial...

Hi Kashliks,

If you want to try the trial license for CLC bio's Genomics Workbench, it includes access to a variety of tutorials that are laced with references to foundation publications. It would...
Forum: Bioinformatics 10-15-2011, 12:54 PM
Replies: 65
Views: 29,493
Posted By Nomijill
Just for everyone who is using the Genomics...

Just for everyone who is using the Genomics Workbench to know - There have been numerous updates to the functionality. Much of which is available as a plug-in download. For the de novo assembler...
Forum: General 05-10-2011, 06:27 PM
Replies: 3
Views: 1,193
Posted By Nomijill
In response to New2Sequencing

Hi New2Sequencing -

Please excuse me if I tell you things you already know. I figure better that way than the reverse.

The type of analysis problem that you have depends on whether or not you...
Forum: Bioinformatics 11-21-2010, 05:14 PM
Replies: 1
Views: 2,662
Posted By Nomijill
Dear BardJ. Sorry about the late answer. I was...

Dear BardJ. Sorry about the late answer. I was just splunking through SeqAnswers, and I found your question. Hybrid assemblies are a common use of the Workbench. I can send you a publication that...
Forum: Bioinformatics 08-30-2010, 05:53 AM
Replies: 15
Views: 7,508
Posted By Nomijill
miRNA analysis - making it better!

Hi Anelda-

You are right. I looked at your record and I saw your e-mails with your recommendations for improving the miRNA functions. Thanks for passing that on. I am sure your feedback has been...
Forum: Bioinformatics 08-29-2010, 08:26 PM
Replies: 40
Views: 13,210
Posted By Nomijill
Hi all, For the indels that you are looking...

Hi all,

For the indels that you are looking for, what are your read lengths and what are the sizes of the indels you expect to find?

Thanks,
Naomi
Forum: Bioinformatics 08-29-2010, 08:20 PM
Replies: 15
Views: 7,508
Posted By Nomijill
commercial miRNA analysis pipeline

Dear Nicholas,

Please let me know what you think about the CLC bio miRNA analysis pipeline. We released it in version 4.0 in June. The feedback that we have had, especially for its speed and ease...
Forum: Bioinformatics 08-16-2010, 07:14 PM
Replies: 28
Views: 12,739
Posted By Nomijill
Thumbs up Really easy to use microRNA tool

Caution: I work for CLC bio

If any of you would like to try a very easy to use tool for microRNA analysis, the 4.0 version of CLC bio's Genomics Workbench includes a start (trimming adapters) to...
Forum: Bioinformatics 08-12-2010, 07:13 PM
Replies: 12
Views: 2,873
Posted By Nomijill
Display of confidence scores

You should be able to view the quality scores of all of your bases in the Genomics Workbench. It is a display option. If you want, I can show you how.:)
Forum: Bioinformatics 07-10-2010, 01:26 PM
Replies: 3
Views: 1,262
Posted By Nomijill
Thumbs up multiple reference sequences

I do not know if you have tried the CLC bio software at all, but it should be able to handle your data in a variety of ways. First, you can easily map your Illumina reads to multiple reference...
Forum: Bioinformatics 06-16-2010, 11:16 AM
Replies: 24
Views: 11,347
Posted By Nomijill
new miRNA software

Hi,

I don't know if this would be helpful to you, but CLC just released a new version of our Genomics Workbench and the most significant added functionality is a suite of tools to support miRNA...
Forum: Introductions 06-16-2010, 10:29 AM
Replies: 1
Views: 686
Posted By Nomijill
Cool Hello Summer Student

I envy you the opportunity to get involved in this exciting technology so early in your career. The quantity of data is overwhelming with NextGen sequencing, but so is its potential. This Forum is a...
Forum: Bioinformatics 04-16-2010, 11:18 AM
Replies: 5
Views: 7,122
Posted By Nomijill
I have only heard about BFAST and not yet had a...

I have only heard about BFAST and not yet had a chance to use it, but everything I heard at the NowGen conference was really positive. In this field, where we are all seeking to extract the greatest...
Forum: Bioinformatics 02-03-2010, 03:48 AM
Replies: 19
Views: 23,479
Posted By Nomijill
Duplicate removal

Hi,

I am educating myself on duplicate removal. Why/How is Picard better than Samtools?

Thanks.
Forum: 454 Pyrosequencing 12-30-2009, 07:48 AM
Replies: 12
Views: 11,846
Posted By Nomijill
What is the expected cost per base from Junior?

What is the expected cost per base from Junior?
Forum: Bioinformatics 12-13-2009, 03:23 PM
Replies: 33
Views: 14,955
Posted By Nomijill
This is great thank you.

This is great thank you.
Forum: Bioinformatics 12-10-2009, 08:03 PM
Replies: 236
Views: 504,325
Posted By Nomijill
Sciguy, I notice that you last updated your list...

Sciguy, I notice that you last updated your list in August. Are there any significant changes since then? Or am I wrong about the reading of the update?
Forum: Bioinformatics 12-04-2009, 06:56 AM
Replies: 6
Views: 4,578
Posted By Nomijill
Disclosure: I used to work for Gene Codes ...

Disclosure: I used to work for Gene Codes

Has anyone used Sequencher for Nextgen analysis?
Forum: Bioinformatics 12-04-2009, 04:03 AM
Replies: 1
Views: 3,118
Posted By Nomijill
Question Help: I need to speak to an expert in commercial DNA analysis applications

I am in need of an expert opinion from someone who is familiar with a broad range of commercial DNA analysis applications. If you are this person, or if you know of someone, please contact me. I can...
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