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Search: Posts Made By: mucku
Forum: Literature Watch 07-01-2011, 05:21 AM
Replies: 2
Views: 2,472
Posted By mucku
Question Is it only me or are there some inaccuracies in...

Is it only me or are there some inaccuracies in that review?

>> Helicos "Read lengths - Longer than 1000" and other things...
Forum: General 07-01-2011, 05:14 AM
Replies: 3
Views: 3,108
Posted By mucku
I guess you are right... the generation length...

I guess you are right... the generation length has probably become too short anyways with all the new sequencing methods popping up... let's just call it post-Sanger sequencing...
Forum: General 07-01-2011, 01:21 AM
Replies: 3
Views: 3,108
Posted By mucku
Question Is there a clear definition of 3rd generation sequencing?

Hi,

I have a question...
Is there a real definition of what 3rd generation sequencing is? :confused:
Or is it just depending on which company you ask? Some say single molecule sequencing is 3rd...
Forum: General 06-19-2011, 09:53 PM
Replies: 39
Views: 24,257
Posted By mucku
Sorry if it came across that I stated it doesn't...

Sorry if it came across that I stated it doesn't have any problems... I have to apologize.
At this point there is so much competition in that area that probably only half of the information...
Forum: General 06-18-2011, 03:58 AM
Replies: 39
Views: 24,257
Posted By mucku
I found these webinars of IonTorrent very...

I found these webinars of IonTorrent very informative.

They also show data from the Broad Institute and others...
...
Forum: General 06-17-2011, 04:42 AM
Replies: 39
Views: 24,257
Posted By mucku
- PGM : 10Mb (314 chip), 100Mb (316 chip), 1Gb...

- PGM : 10Mb (314 chip), 100Mb (316 chip), 1Gb (318 chip)
- MiSeq : 680Mb (2X100), 1Gb (2X150)
- GS Junior : 1Gb, 500bp max by amplicon

I have to correct your GS Junior statement:

The...
Forum: Bioinformatics 12-15-2010, 11:53 AM
Replies: 3
Views: 1,416
Posted By mucku
My scripting skills are the problem... I know...

My scripting skills are the problem... I know some basic shell stuff like grep, sed, awk etc. I come more from the wetlab. Using pre-existing tools and some mild reformatting is ok for me. But I am...
Forum: Bioinformatics 12-15-2010, 04:04 AM
Replies: 3
Views: 1,416
Posted By mucku
Question Splitting fasta AND quality on masked sequence

Hello,
does anybody have a script or any program that allows me to split fasta sequences and the according quality file on masked bases such as "N"? Everything I find works perfectly on fasta files...
Forum: De novo discovery 08-04-2010, 10:03 PM
Replies: 58
Views: 49,802
Posted By mucku
Hello, One question. Is Velvet mandatory for...

Hello,
One question.
Is Velvet mandatory for Oases or can the contigs be derived from a different short read assembler such as ABySS?

Cheers

Markus
Forum: Bioinformatics 10-27-2009, 03:53 AM
Replies: 13
Views: 4,074
Posted By mucku
Hi. I thought I already did send you a private...

Hi. I thought I already did send you a private message montera. CAP3 is also included in the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3....
Forum: Bioinformatics 10-27-2009, 03:50 AM
Replies: 13
Views: 4,074
Posted By mucku
I thought i sent you a message montera. CAP3...

I thought i sent you a message montera.
CAP3 is also part of the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3 too.
Forum: Bioinformatics 10-27-2009, 12:35 AM
Replies: 13
Views: 4,074
Posted By mucku
That's funny... my question is like 9 months old....

That's funny... my question is like 9 months old. Then "montera" asked for CAP3 and suddenly the answers are popping up. Well I will try CONSED although I don't need this anymore at this moment.
...
Forum: Bioinformatics 10-26-2009, 12:13 PM
Replies: 13
Views: 4,074
Posted By mucku
Hello, CAP3 is also part of the TGICL package....

Hello,
CAP3 is also part of the TGICL package. So you can just download it and use CAP3 from it. For which operating system do you need it for? It's also available as a Biolinux package.
...
Forum: Bioinformatics 01-21-2009, 12:44 PM
Replies: 13
Views: 4,074
Posted By mucku
Unhappy CAP3 output *.ace in EagleView?

Hello,
I am a molecular biologist. We have done some EST sequencing and I used TGICL / CAP3 for sequence assembly. Everything works fine and it constructs all the contigs etc. Now I wanted to check...
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