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Search: Posts Made By: rskr
Forum: Bioinformatics 01-16-2018, 05:53 PM
Replies: 9
Views: 10,994
Posted By rskr
I think now you can do both at the same time. ...

I think now you can do both at the same time. HISAT2 builds suffix indexes with annotations built in, so whichever mapping best explains the data are chosen. :)
Forum: Bioinformatics 07-11-2014, 02:48 PM
Replies: 7
Views: 2,271
Posted By rskr
I use Cramer's V for heatmap it is a measure of...

I use Cramer's V for heatmap it is a measure of association that that doesn't suffer from being over generalized from continuous variables to discrete variables, and actually makes sense when...
Forum: Academic/Non-Profit Jobs 07-04-2014, 05:10 AM
Replies: 20
Views: 2,867
Posted By rskr
I agree with you, many single skilled programmers...

I agree with you, many single skilled programmers don't have this perspective. However in the context of a skills inventory, C++ is a superior skill. Most of these open source programs were written...
Forum: Academic/Non-Profit Jobs 07-03-2014, 01:06 PM
Replies: 20
Views: 2,867
Posted By rskr
We may be in violent agreement here, but as I...

We may be in violent agreement here, but as I said earlier. Java is a trivial skill java programmers don't even have to know I/O...
Forum: Academic/Non-Profit Jobs 07-03-2014, 04:26 AM
Replies: 20
Views: 2,867
Posted By rskr
Please go look up GTK then communicate to the...

Please go look up GTK then communicate to the world your ability to learn a how java uses a C library to do graphics.
Forum: Academic/Non-Profit Jobs 07-02-2014, 04:18 PM
Replies: 20
Views: 2,867
Posted By rskr
Sure, but how many times have you read the...

Sure, but how many times have you read the library it was calling into because the feature wasn't documented well enough in the cheesy vignette? A great example is how does the corr function handle...
Forum: Academic/Non-Profit Jobs 07-02-2014, 02:44 PM
Replies: 20
Views: 2,867
Posted By rskr
I've noticed a couple trends. One is kind of...

I've noticed a couple trends. One is kind of like multi skilled players trend in basketball, shooting centers, point forwards, combo guards, swing men, etc. as has has been noted by sports...
Forum: Bioinformatics 03-16-2014, 07:05 PM
Replies: 26
Views: 8,325
Posted By rskr
IMO it is obvious that Tophat went to...

IMO it is obvious that Tophat went to transcriptome mapping because they were unable to solve the pseudo gene problem, what remains to be seen is does using the genome actually bring anything to the...
Forum: Bioinformatics 03-16-2014, 06:30 AM
Replies: 26
Views: 8,325
Posted By rskr
Well, never do genome mapping because you'll...

Well, never do genome mapping because you'll spend more time studying pseudo genes. Now, what are you going to do?

Anyway it doesn't make sense to me that you would get isoforms via genome...
Forum: Bioinformatics 02-24-2014, 04:51 PM
Replies: 26
Views: 8,325
Posted By rskr
Right that's what arrays are for, but in a...

Right that's what arrays are for, but in a limited and expensive manner.;)
Forum: Bioinformatics 02-24-2014, 05:17 AM
Replies: 26
Views: 8,325
Posted By rskr
I think there is more to it than having or not...

I think there is more to it than having or not having compute power. I've found mappings to transcriptomes to be much cleaner, the biggest culprit in genome mappings are pseudo genes. Furthermore,...
Forum: Bioinformatics 02-21-2014, 01:37 PM
Replies: 2
Views: 832
Posted By rskr
I thought cufflinks would do something similar. ...

I thought cufflinks would do something similar. Maybe generate a transcriptome fasta file that could then be re-mapped. I think a tool like this would be very useful though, since working in the...
Forum: General 02-12-2014, 06:50 AM
Replies: 7
Views: 1,647
Posted By rskr
Microarray Replicate vs Sequencing cost break even point.

As has been mentioned in several threads, Microarray slides are cheaper but require more technical replicates than RNA-seq. I wonder what the cost point is where the one or more RNA-seq runs are...
Forum: Introductions 02-12-2014, 05:08 AM
Replies: 3
Views: 983
Posted By rskr
I think a PhD in bioinformatics is unnecessary,...

I think a PhD in bioinformatics is unnecessary, though some might pipe up and say they derived enormous benefit from putting together a piecemeal thesis analyzing other peoples data. However, it...
Forum: Bioinformatics 02-11-2014, 06:51 AM
Replies: 4
Views: 1,756
Posted By rskr
I just want to emphasize that blasting...

I just want to emphasize that blasting transcriptomes against each other is especially naive, since it is fundamentally a local alignment, and any results generated thusly would be highly suspect. ...
Forum: Bioinformatics 02-04-2014, 09:33 AM
Replies: 6
Views: 2,360
Posted By rskr
I wouldn't normalize anything, but using...

I wouldn't normalize anything, but using housekeeping genes to verify your statistical model might not be a bad idea.
Forum: Bioinformatics 02-04-2014, 06:36 AM
Replies: 6
Views: 2,360
Posted By rskr
Since with sequencing, there is much more...

Since with sequencing, there is much more confidence in the observations, which have a built in noise check during the mapping, and it is necessary to account for the overall differences in reads...
Forum: Bioinformatics 01-31-2014, 07:33 AM
Replies: 2
Views: 2,157
Posted By rskr
Good numerical analysts and mathematicians do...

Good numerical analysts and mathematicians do delta epsilon proofs to figure out what a mathematically undefined quantity should be in specific cases to provide continuity, then redefine the...
Forum: Bioinformatics 01-27-2014, 12:39 PM
Replies: 23
Views: 49,828
Posted By rskr
I don't know for sure. I first noticed the...

I don't know for sure. I first noticed the problem doing some meta-analysis hypothesis testing on coverage merging p-values of bases with each base having a different statistical power. Using...
Forum: Bioinformatics 01-27-2014, 11:15 AM
Replies: 23
Views: 49,828
Posted By rskr
Low coverage genes can still be significant, just...

Low coverage genes can still be significant, just not at the same rate as the higher coverage genes, though it may be possible to filter out certain genes which have zero chance of being significant,...
Forum: Bioinformatics 01-27-2014, 09:55 AM
Replies: 23
Views: 49,828
Posted By rskr
I don't think FDR is very important for RNA-seq. ...

I don't think FDR is very important for RNA-seq. For multiple hypothesis tests where each test has uniform variance and is sufficiently powered, FDR might be OK, however for the counts data FDR...
Forum: General 01-12-2014, 11:33 AM
Replies: 9
Views: 5,152
Posted By rskr
Thats all fine and good except its only three...

Thats all fine and good except its only three months after a government shutdown, and less than a year after significant reduction in budget called a sequester, and during an ongoing hiring freeze....
Forum: General 01-10-2014, 07:43 AM
Replies: 9
Views: 5,152
Posted By rskr
I guess they really just can't find Americans to...

I guess they really just can't find Americans to do it that cheaply.

http://hh.ru/vacancy/7096038?utm_content=Russia&utm_medium=meta&utm_source=indeed&utm_campaign=Indeed
Forum: De novo discovery 01-10-2014, 04:55 AM
Replies: 3
Views: 1,851
Posted By rskr
It's too bad SGA is still in experimental phase,...

It's too bad SGA is still in experimental phase, and it appears that it is making genome type assumptions about coverage, otherwise for read correcting and data reduction it is an awesome assembler. ...
Forum: General 01-08-2014, 06:08 PM
Replies: 9
Views: 5,152
Posted By rskr
For most positions the difference between the top...

For most positions the difference between the top candidates is negligible, that's why bias is so pervasive, if there is any perceived problem with diversity then it must be a problem with the...
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