Forum: Vendor Forum
05-26-2016, 07:51 PM
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Replies: 10
Views: 8,867
Strand specificity
Hi, just to clarify a question about strand specficity.
In Illumina Truseq system, the + strand is digested and the - strand is retained, and that's how strand specificity is maintained, such that...
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Forum: Bioinformatics
02-03-2016, 02:52 PM
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Replies: 8
Views: 3,850
Thanks for the feedback! To answer your...
Thanks for the feedback! To answer your questions:
1) For future releases, we will include citation information, but for now, please cite:
Jones,D., Stuckey, A., and Fan, V. (2016)....
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Forum: Bioinformatics
01-25-2016, 01:45 PM
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Replies: 8
Views: 3,850
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Forum: Bioinformatics
01-25-2016, 12:40 PM
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Replies: 8
Views: 3,850
Hi, thanks for your reply. I'm not able to...
Hi, thanks for your reply. I'm not able to replicate this error. If you mean this error:
error in evaluating the argument 'object' in selecting a method for function 'expressionPlot': Error in...
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Forum: RNA Sequencing
01-24-2016, 08:25 PM
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Replies: 5
Views: 2,168
While trinity is obviously not relevant for...
While trinity is obviously not relevant for humans, this vid explains strand specficity quite well:
https://www.youtube.com/watch?v=n2XEsw7EJLw
You will likely miss antisense transcription...
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Forum: RNA Sequencing
01-24-2016, 08:12 PM
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Replies: 4
Views: 3,413
That's not what the -G option does. It means...
That's not what the -G option does. It means "only quantitate against genes supplied in the GTF file". While -g means "assemble new genes as well, if there is read support, and quantitate them too"....
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Forum: RNA Sequencing
01-24-2016, 08:07 PM
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Replies: 2
Views: 2,981
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Forum: RNA Sequencing
01-24-2016, 07:59 PM
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Replies: 0
Views: 1,933
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Forum: Bioinformatics
01-24-2016, 06:50 PM
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Replies: 8
Views: 3,850
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Forum: Bioinformatics
11-23-2015, 01:26 PM
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Replies: 12
Views: 7,493
Hi, thanks for this contribution..
I'm...
Hi, thanks for this contribution..
I'm reading the code, and this is what it looks like to me, but am I correct in saying that this script would correctly deduplicate splice-aware mappings ? i.e....
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Forum: Illumina/Solexa
10-09-2015, 03:55 PM
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Replies: 18
Views: 6,309
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Forum: Illumina/Solexa
10-09-2015, 03:20 PM
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Replies: 18
Views: 6,309
thanks for the response...
Thanks for the response, but this does not answer my questions and nor does any of the information in the qRNA-Analysis.pdf white paper. Some of the terminology in the description of the dqRNASeq...
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Forum: Illumina/Solexa
10-08-2015, 06:15 PM
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Replies: 18
Views: 6,309
re-adding stochastic labels
Can I ask for specifics about how, exactly, you re-add the stochastic labels (which I assume is the same as the 8bp molecular index at the start) to "mapped reads" (= Bam file?? Sorted how?)?
Or do...
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Forum: Bioinformatics
10-08-2015, 06:08 PM
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Replies: 12
Views: 7,493
Molecular indexing
Hi, you could try the script mentioned here:
http://www.biooscientific.com/Portals/0/White%20Papers/qRNA-Analysis.pdf
It's currently not working for me, but I'm in communication with the...
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Forum: Bioinformatics
07-29-2015, 09:07 PM
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Replies: 1
Views: 1,741
I'm not an expert but if your replicates are...
I'm not an expert but if your replicates are closer to replicates from another condition than they are to each other, I can see a problem. Surely replicates from a single condition should cluster?
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Forum: De novo discovery
11-19-2014, 02:48 PM
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Replies: 8
Views: 3,036
My understanding is yes
Actually don't...
My understanding is yes
Actually don't know.
MIRA4 works by using a manifest file that defines the data to go into the program.
look at section 5.3.3. Manifest for data sets with paired...
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Forum: De novo discovery
11-19-2014, 01:45 PM
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Replies: 8
Views: 3,036
MIRA4: ...
MIRA4:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_denovo
Can handle hybrid assemblies, and also can handle paired-end reads in the orientation you describe...
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Forum: RNA Sequencing
10-29-2014, 06:10 PM
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Replies: 3
Views: 1,906
That particular study from the SRA used five...
That particular study from the SRA used five platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS) so I'd be curious as to...
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Forum: RNA Sequencing
10-29-2014, 04:11 PM
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Replies: 34
Views: 5,618
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Forum: RNA Sequencing
10-29-2014, 03:25 PM
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Replies: 6
Views: 3,449
This is definitely a hard one. I can see all...
This is definitely a hard one. I can see all sorts of problems comparing expression levels between genes that are not exactly the same. Yes, you could get a number for gene 1 and a number for gene 2,...
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Forum: RNA Sequencing
10-29-2014, 03:12 PM
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Replies: 34
Views: 5,618
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Forum: RNA Sequencing
10-29-2014, 02:28 PM
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Replies: 34
Views: 5,618
You can use the -r option to set the known size...
You can use the -r option to set the known size of the insert, and there are also options to set the standard deviation of the size. Size selection is done on a Covaris or simply on a agarose gel,...
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Forum: RNA Sequencing
10-28-2014, 08:53 PM
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Replies: 34
Views: 5,618
You should know both the library type and the...
You should know both the library type and the size of the fragments that were selected and sequenced. This should be info that the sequencing provider gives you, and if they don't, they are doing you...
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Forum: RNA Sequencing
10-28-2014, 08:10 PM
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Replies: 34
Views: 5,618
I still don't understand why you want to use a...
I still don't understand why you want to use a non-splice-aware mapper at all, since every mRNA-derived read that spans a splice junction will fail to map properly. Why use Bowtie or SNAP at all? It...
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Forum: RNA Sequencing
10-28-2014, 06:44 PM
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Replies: 34
Views: 5,618
Also:
While I understand that this...
Also:
While I understand that this happens occasionally and it's sometimes not under your control, this is a terrible situation and if you can get as much information on the context of the run...
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