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Forum: Bioinformatics 07-21-2019, 08:03 PM
Replies: 8
Views: 1,053
Posted By robp
Hi tamu_anand, I think this is an...

Hi tamu_anand,

I think this is an interesting question, and one that I'm not certain has a clearly "right" or "wrong" answer. While peer-review and publication of the paper associated with a...
Forum: RNA Sequencing 01-26-2016, 04:38 AM
Replies: 8
Views: 3,479
Posted By robp
RSEM cannot handle alignments with gaps in them;...

RSEM cannot handle alignments with gaps in them; only matches / mis-matches. I would suggest that you use the alignment-based mode of salmon (https://github.com/COMBINE-lab/salmon) if you'd still...
Forum: Bioinformatics 05-22-2015, 09:11 AM
Replies: 2
Views: 2,181
Posted By robp
Hi seversond12, I just came across this...

Hi seversond12,

I just came across this post. Did you ever track down the source of these differences? I'd be interested in knowing. Also, was this salmon result with / without bias...
Forum: Bioinformatics 02-26-2015, 04:40 PM
Replies: 5
Views: 3,743
Posted By robp
It looks pretty good from the paper, and I'd...

It looks pretty good from the paper, and I'd definitely give StringTie a shot, but I've not tested the software yet. However, if you're looking to try out a new tool, I'd also take a look at the...
Forum: Bioinformatics 12-18-2014, 08:11 AM
Replies: 0
Views: 2,051
Posted By robp
Salmon: A fast and versatile new tool for RNA-seq quantification

Hi all,

I'd like to let you all know about Salmon, a new tool we've been developing for isoform-level quantification from RNA-seq data. It is, conceptually, the successor to our Sailfish...
Forum: Oxford Nanopore 10-10-2014, 05:31 PM
Replies: 47
Views: 17,289
Posted By robp
Hi ymc, Certainly in the short term, I...

Hi ymc,

Certainly in the short term, I don't think that long read technology will replace Illumnia-style technology for quantification. The problems tackled by long reads are different. It may...
Forum: Oxford Nanopore 10-01-2014, 09:45 PM
Replies: 47
Views: 17,289
Posted By robp
Hi Brian, I agree with you (i.e. that a...

Hi Brian,

I agree with you (i.e. that a zero probability would be a bad idea here). For example, there are almost certainly, e.g. incidents of slippage in the molecule, speed-ups, slow-downs,...
Forum: Oxford Nanopore 10-01-2014, 07:03 PM
Replies: 47
Views: 17,289
Posted By robp
I'm not quite sure I understand the reasoning...

I'm not quite sure I understand the reasoning here. We could have a model with 4^5 states, but there is only a non-zero probability of transition between consistent k-mers. For example, the state...
Forum: Oxford Nanopore 09-28-2014, 08:14 AM
Replies: 47
Views: 17,289
Posted By robp
Well, again, we don't really know because the...

Well, again, we don't really know because the software that does the base-calling is actually remote (on the cloud, I believe) and proprietary. So, we don't really know what's in the model files or...
Forum: Oxford Nanopore 09-28-2014, 07:04 AM
Replies: 47
Views: 17,289
Posted By robp
Yea, I agree. It's an interesting computational...

Yea, I agree. It's an interesting computational problem (I'm a computer scientist by trade), and I can think of at least a few ways an HMM-based base caller could be improved and a few other ways a...
Forum: Oxford Nanopore 09-27-2014, 11:15 AM
Replies: 47
Views: 17,289
Posted By robp
Hi Nick! First, thanks for getting the...

Hi Nick! First, thanks for getting the manuscript out there as a pre-print. Also, thanks for making the data available in all it's glory. I am curious if you know if ONT's basecaller is publicly...
Forum: Oxford Nanopore 09-26-2014, 05:50 PM
Replies: 47
Views: 17,289
Posted By robp
I also think an algorithm for dealing with this...

I also think an algorithm for dealing with this would give rise to a very interesting CS paper. I'd be willing to bet that changes in molecular speed affect the resulting signal in detectable ways,...
Forum: Bioinformatics 08-23-2013, 10:07 AM
Replies: 10
Views: 14,365
Posted By robp
That's a very concise solution! However, I think...

That's a very concise solution! However, I think that the commands should be:


sed -ne '1~8{N;N;N;p}' x.fastq > x_1.fastq
sed -ne '5~8{N;N;N;p}' x.fastq > x_2.fastq


Where, for the second...
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