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Search: Posts Made By: Symphysodon
Forum: Bioinformatics 10-19-2011, 03:30 AM
Replies: 4
Views: 15,752
Posted By Symphysodon
Hi, Thanks maubp and rskr for your feedback....

Hi,

Thanks maubp and rskr for your feedback.

I am using blastn from blastall 2.2.23 and blastn from BLAST+ 2.2.25.

Perhaps if I specify for both to use the same hash word size, that might be...
Forum: Bioinformatics 10-18-2011, 02:24 AM
Replies: 4
Views: 15,752
Posted By Symphysodon
BLAST+ vs BLASTALL (legacy BLAST)

Hi all,

I have done a comparison of blastn as implemented in BLAST+ 2.2.25 (latest version) and BLASTALL (legacy BLAST) and observed non-trivial discrepancies in the results. In summary, BLAST+...
Forum: De novo discovery 03-08-2011, 07:31 PM
Replies: 58
Views: 50,300
Posted By Symphysodon
I have total of a little over 22 million...

I have total of a little over 22 million 99-nucleotide reads. This is from four lanes of Illumina data.

I have just assembled one lane of data (5,522,680) and Oases seems to be able to cope with...
Forum: De novo discovery 03-06-2011, 11:54 PM
Replies: 58
Views: 50,300
Posted By Symphysodon
Thanks for your suggestions re. Oases:...

Thanks for your suggestions re. Oases: segmentation fault.

I have recompiled Oases, making sure to give the correct path to Velvet and specifying the same 'CATEGORIES=30' 'MAXKMERLENGTH=99' as for...
Forum: De novo discovery 03-06-2011, 09:29 PM
Replies: 58
Views: 50,300
Posted By Symphysodon
Oases: segmentation fault

Hi all,

I'm trying to use Oases to do a de novo transcriptome assembly of single-end Illumina reads, but am getting the following error message:

[0.000000] Reading graph file...
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