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Search: Posts Made By: KanyeDidIt
Forum: Bioinformatics 06-20-2011, 06:44 AM
Replies: 252
Views: 102,213
Posted By KanyeDidIt
Hi Boetsie, Just out of curiosity is this...

Hi Boetsie,

Just out of curiosity is this script written in 32 bit perl? I see an issue with the program not taking beyond a certain level of memory.
Forum: Bioinformatics 06-08-2011, 08:34 AM
Replies: 252
Views: 102,213
Posted By KanyeDidIt
edited after solution

edited after solution
Forum: Bioinformatics 04-22-2011, 04:54 PM
Replies: 4
Views: 2,076
Posted By KanyeDidIt
If the contigs are in Pcap format its kind of...

If the contigs are in Pcap format its kind of easy to indentify the contig - scaffold relationship.

Contig5.1, Contig5.2..... should belong to Scaffold5. Something similar to that. This can be...
Forum: Bioinformatics 03-21-2011, 07:36 AM
Replies: 4
Views: 2,076
Posted By KanyeDidIt
You need to write a simple script with perl to...

You need to write a simple script with perl to produce a read.placed.original file in the format that comes with the example file.
Forum: Bioinformatics 02-24-2011, 08:12 AM
Replies: 5
Views: 1,269
Posted By KanyeDidIt
Yes if you also have illumina reads to align them...

Yes if you also have illumina reads to align them to.

http://genomebiology.com/2010/11/4/R41

That's the paper on IMAGE2, it should help.
Forum: Bioinformatics 02-24-2011, 07:52 AM
Replies: 5
Views: 1,269
Posted By KanyeDidIt
You normally need fastq reads and a fasta...

You normally need fastq reads and a fasta sequence to run IMAGE2.
Forum: Bioinformatics 02-24-2011, 07:23 AM
Replies: 5
Views: 1,269
Posted By KanyeDidIt
Generating base quality information after sequence improvement

Hi all,

We've tried using IMAGE2 for closing gaps on an assembly and so far have got very impressive results with respect to closing gaps and also improving contig stats.

I just wanted to know...
Forum: Bioinformatics 09-15-2010, 08:42 AM
Replies: 0
Views: 1,383
Posted By KanyeDidIt
Exclamation Satsuma alingment tool

Hi,

Just wanted to know if any of you have experience using Satsuma alignment tool that comes as part of the Spines package developed by Broad/MIT.

I'm trying to do a test run right now and am...
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