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Search: Posts Made By: lskatz
Forum: Bioinformatics 03-07-2016, 07:03 AM
Replies: 2
Views: 844
Posted By lskatz
There are many comparison metrics. I have been...

There are many comparison metrics. I have been looking into the Kendall-Colijn metric recently and am trying to port it to an Rscript at my github site...
Forum: Illumina/Solexa 10-24-2011, 09:30 AM
Replies: 3
Views: 4,666
Posted By lskatz
Nevermind; I just had to upgrade from my 2008...

Nevermind; I just had to upgrade from my 2008 version.
Forum: Illumina/Solexa 10-24-2011, 08:44 AM
Replies: 3
Views: 4,666
Posted By lskatz
I would LOVE to know the answer to this, because...

I would LOVE to know the answer to this, because I always get this error message.
Forum: Bioinformatics 11-22-2010, 08:20 AM
Replies: 5
Views: 2,935
Posted By lskatz
It's down there at the end. If you think it's...

It's down there at the end. If you think it's helpful I'll send again to the list with all those details.
http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034275.html

My OS is Ubuntu...
Forum: Bioinformatics 11-22-2010, 07:44 AM
Replies: 5
Views: 2,935
Posted By lskatz
Yes I've tried telling it that it is a 454 Ace...

Yes I've tried telling it that it is a 454 Ace file, using both the variant syntax and the ace-454 syntax. I get the error using either one.

I asked the mailing list at the end of last week, but...
Forum: Bioinformatics 11-22-2010, 06:27 AM
Replies: 5
Views: 2,935
Posted By lskatz
How do I convert 454 ace to a regular ace?

I have read on the BioPerl site that a 454 ace is not standardized due to its coordinate system. How can I convert it to the standard ace file?

When I run this code either by using contig or...
Forum: Bioinformatics 10-19-2010, 07:21 PM
Replies: 11
Views: 3,315
Posted By lskatz
Doesn't BLAST rest on a C library of some sort? ...

Doesn't BLAST rest on a C library of some sort? And they just refactored it according to their 2009 BLAST+ paper.
Forum: Bioinformatics 10-07-2010, 04:41 PM
Replies: 0
Views: 1,716
Posted By lskatz
Unhappy Sanger/WashU format

What is Sanger/WashU format? Is there a tool for converting assembly output to this format? I have Newbler output (fna, qual, etc).

I have been trying to use an interesting tool called the...
Forum: General 09-30-2010, 07:00 AM
Replies: 2
Views: 3,896
Posted By lskatz
What is everyone's opinion about Opgen? I believe...

What is everyone's opinion about Opgen? I believe their mapping software is called MapIt. I have been asked to use Opgen data with 454 and am wondering what everyone's experience is before I go using...
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