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Forum: Bioinformatics 03-08-2012, 03:15 PM
Replies: 5
Views: 2,189
Posted By Rockx
Hi, I am working with guru1985 on this project. ...

Hi, I am working with guru1985 on this project.

The error is occuring when SOAPdenovo starts to fill the scaffold gaps with reads from the *.ReadInGap file.

From the error message "...0 0 0...
Forum: Bioinformatics 12-18-2011, 07:17 PM
Replies: 0
Views: 2,515
Posted By Rockx
Genemark-ES and Maker

Hi all,

I've run the MAKER gene annotation pipeline using Genemark for ab-initio gene predictions. However, it seems like Genemark is reporting each gene twice. Does anyone know why this is...
Forum: Bioinformatics 12-12-2011, 02:55 PM
Replies: 9
Views: 2,325
Posted By Rockx
Thanks maubp and swbarnes2. Indeed, I did end up...

Thanks maubp and swbarnes2. Indeed, I did end up editing the DynamicTrim perl script to include and option for GC trimming, this deals with paired end data fine.

swbarnes2, thanks for this tip....
Forum: Bioinformatics 12-07-2011, 10:43 PM
Replies: 18
Views: 6,604
Posted By Rockx
For a denovo assembly, I guess you could use the...

For a denovo assembly, I guess you could use the GC filter to assemble a draft genome. You could then use this draft as a reference for future assemblies using contigs filtered using other methods,...
Forum: Bioinformatics 12-07-2011, 09:02 PM
Replies: 18
Views: 6,604
Posted By Rockx
How would you deal with gene transfer in these...

How would you deal with gene transfer in these instances? Horizontally acquired genes would have a different GC content, which would be eliminated using GC and blast binning.
Forum: Bioinformatics 12-07-2011, 03:07 PM
Replies: 1
Views: 2,301
Posted By Rockx
PRINSEQ and paired-end data

Hi, I am using PRINSEQ to separate reads of differing GC content, however I have noticed that it doesn't deal with paired-end data.

Is there any software that can separate reads based on GC using...
Forum: Bioinformatics 12-06-2011, 03:38 PM
Replies: 9
Views: 2,325
Posted By Rockx
I am also having the same problem. What...

I am also having the same problem.

What programs should I be using to separate reads based on GC content? A search of these forums only revealed replies such as "there are many programs that do...
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