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Search: Posts Made By: danwiththeplan
Forum: Vendor Forum 05-26-2016, 06:51 PM
Replies: 10
Views: 7,953
Posted By danwiththeplan
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...
Forum: Bioinformatics 02-03-2016, 01:52 PM
Replies: 8
Views: 2,880
Posted By danwiththeplan
Thumbs up 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)....
Forum: Bioinformatics 01-25-2016, 12:45 PM
Replies: 8
Views: 2,880
Posted By danwiththeplan
Great, thanks, this is now fixed. Prettier plots...

Great, thanks, this is now fixed. Prettier plots (using ggplot2) are definitely a plan for the near future. Hoping to get publication-level plots that can be generated on the fly. To avoid spamming...
Forum: Bioinformatics 01-25-2016, 11:40 AM
Replies: 8
Views: 2,880
Posted By danwiththeplan
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...
Forum: RNA Sequencing 01-24-2016, 07:25 PM
Replies: 5
Views: 1,843
Posted By danwiththeplan
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...
Forum: RNA Sequencing 01-24-2016, 07:12 PM
Replies: 4
Views: 3,070
Posted By danwiththeplan
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"....
Forum: RNA Sequencing 01-24-2016, 07:07 PM
Replies: 2
Views: 2,318
Posted By danwiththeplan
XLOC numbers are assigned to all genes, not just...

XLOC numbers are assigned to all genes, not just ones that aren't in GTF files you supply. So some genes will end up with a gene_name, but all genes end up with a gene_id (=XLOC number). I think the...
Forum: RNA Sequencing 01-24-2016, 06:59 PM
Replies: 0
Views: 1,384
Posted By danwiththeplan
shiny_cuffdiff: On-the-fly interrogation and plotting of gene expression results

Hi all. I'd like to introduce the community to shiny_cuffdiff

http://nzgl.github.io/shiny_cuffdiff/

Put simply, this code uses the outputs of the Tuxedo workflow (Tophat2 > Cufflinks >...
Forum: Bioinformatics 01-24-2016, 05:50 PM
Replies: 8
Views: 2,880
Posted By danwiththeplan
shiny_cuffdiff: On-the-fly interrogation and plotting of gene expression results

Hi all. I'd like to introduce the community to shiny_cuffdiff

http://nzgl.github.io/shiny_cuffdiff/

Put simply, this code uses the outputs of the Tuxedo workflow (Tophat2 > Cufflinks >...
Forum: Bioinformatics 11-23-2015, 12:26 PM
Replies: 12
Views: 6,305
Posted By danwiththeplan
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....
Forum: Illumina/Solexa 10-09-2015, 02:55 PM
Replies: 18
Views: 5,572
Posted By danwiththeplan
Much appreciated. I think it's a very exciting...

Much appreciated. I think it's a very exciting technology. Easy access to well-documented analysis tools would probably increase uptake.
Forum: Illumina/Solexa 10-09-2015, 02:20 PM
Replies: 18
Views: 5,572
Posted By danwiththeplan
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...
Forum: Illumina/Solexa 10-08-2015, 05:15 PM
Replies: 18
Views: 5,572
Posted By danwiththeplan
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...
Forum: Bioinformatics 10-08-2015, 05:08 PM
Replies: 12
Views: 6,305
Posted By danwiththeplan
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...
Forum: Bioinformatics 07-29-2015, 08:07 PM
Replies: 1
Views: 1,493
Posted By danwiththeplan
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?
Forum: De novo discovery 11-19-2014, 01:48 PM
Replies: 8
Views: 2,672
Posted By danwiththeplan
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...
Forum: De novo discovery 11-19-2014, 12:45 PM
Replies: 8
Views: 2,672
Posted By danwiththeplan
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...
Forum: RNA Sequencing 10-29-2014, 05:10 PM
Replies: 3
Views: 1,678
Posted By danwiththeplan
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...
Forum: RNA Sequencing 10-29-2014, 03:11 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
Yes, seems to be a bit of confusion as to whether...

Yes, seems to be a bit of confusion as to whether GSNAP (post 12) or SNAP (post 21) is producing 46% alignment rate, OP has contradictory posts.
Forum: RNA Sequencing 10-29-2014, 02:25 PM
Replies: 6
Views: 3,061
Posted By danwiththeplan
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,...
Forum: RNA Sequencing 10-29-2014, 02:12 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
Agree totally, and I made this point downthread....

Agree totally, and I made this point downthread. This is why I thought it might be an issue of Tophat being restricted to assembling to known transcripts in the GTF, but apparently that's not the...
Forum: RNA Sequencing 10-29-2014, 01:28 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
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,...
Forum: RNA Sequencing 10-28-2014, 07:53 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
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...
Forum: RNA Sequencing 10-28-2014, 07:10 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
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...
Forum: RNA Sequencing 10-28-2014, 05:44 PM
Replies: 34
Views: 4,599
Posted By danwiththeplan
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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