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Search: Posts Made By: NormSci
Forum: Bioinformatics 09-08-2012, 03:56 PM
Replies: 11
Views: 38,256
Posted By NormSci
Hi Tsuyoshi, After fooling around with...

Hi Tsuyoshi,

After fooling around with blast+ today, I think I've managed to achieve your objective. The command I'm using is:

blastn -query transcripts.fa -out transcripts.blast.txt -task...
Forum: Bioinformatics 07-18-2012, 06:04 AM
Replies: 5
Views: 3,328
Posted By NormSci
Try posting this problem to the Oases mailing...

Try posting this problem to the Oases mailing list:

http://listserver.ebi.ac.uk/mailman/listinfo/oases-users

I believe it is run by DR Zerbino and MA Schultz, the creators of Oases and Velvet....
Forum: RNA Sequencing 07-16-2012, 05:46 PM
Replies: 1
Views: 1,234
Posted By NormSci
Follow-up

For those that may be interested, I spoke with one of the creators of Rnnotator, and the short answer is that the pre-processing step does require large amounts of memory, depending on what options...
Forum: Sample Prep / Library Generation 06-28-2012, 11:40 AM
Replies: 29
Views: 7,480
Posted By NormSci
FYI, from the Epicentre website FAQ...

FYI, from the Epicentre website FAQ (http://www.epibio.com/faq/RiboZero_Kits.asp) RE: Ribozero:
Forum: RNA Sequencing 06-28-2012, 07:59 AM
Replies: 31
Views: 28,812
Posted By NormSci
I completely agree that that DNAse treatment of...

I completely agree that that DNAse treatment of RNA should be standard protocol prior to RNA-seq, and I hope I'm not giving the impression that it is not. It certainly would not be wise to skip this...
Forum: RNA Sequencing 06-26-2012, 06:50 PM
Replies: 31
Views: 28,812
Posted By NormSci
My apologies, perhaps I wasn't clear enough. ...

My apologies, perhaps I wasn't clear enough.

Poly-A repeats matching the oligo-dT primer, that have identical contiguous sequences spanning the entire read length (say, 100 bp), and that occur...
Forum: RNA Sequencing 06-26-2012, 06:22 PM
Replies: 31
Views: 28,812
Posted By NormSci
Unless I am missing something, wouldn't the...

Unless I am missing something, wouldn't the isolation of 3' tail poly-A mRNA (if that is one's goal) filter out any residual DNA contamination? If not, then somebody better tell Illumina to change...
Forum: RNA Sequencing 06-25-2012, 05:35 AM
Replies: 31
Views: 28,812
Posted By NormSci
Naturally, contamination with RNases is the first...

Naturally, contamination with RNases is the first thing one would suspect. To test this I ran control samples (i.e., samples where RNase free H2O was added in place of the requisite reagents...
Forum: Sample Prep / Library Generation 06-13-2012, 01:15 PM
Replies: 1
Views: 1,695
Posted By NormSci
Recommended RIN for RNA-Seq

RNA Integrity Numbers should generally be >= 8 for RNA-Seq. I believe this threshold is recommended by the manufacturer of the BioAnalyzer (Agilent?). Apparently some labs use 7 as a threshold, but...
Forum: RNA Sequencing 06-13-2012, 12:23 PM
Replies: 31
Views: 28,812
Posted By NormSci
Bypass DNase treatment if it is degrading your RNA

I have had similar problems with RNA extractions from gill tissue. Prior to DNase treatment, BioAnalyzer RIN values of my samples were typically > 9, and BioRad Experion RQI values > 8.
...
Forum: RNA Sequencing 06-12-2012, 06:21 PM
Replies: 1
Views: 1,234
Posted By NormSci
Memory requirements for Rnnotator

I am considering using Rnnotator as a pre-processor, primarily to cut down on the enormous memory requirements of the Velvet/Oasis assemblers. However, I can find no information about how much memory...
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