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Search: Posts Made By: steven
Forum: General 05-14-2012, 01:55 AM
Replies: 32
Views: 6,880
Posted By steven
+1 Totally agree - and swapping Python/Perl...

+1
Totally agree - and swapping Python/Perl before R
Forum: Bioinformatics 04-12-2012, 01:40 AM
Replies: 52
Views: 77,853
Posted By steven
As RPKM is a normalized expression measurement so...

As RPKM is a normalized expression measurement so you can in theory directly compare values between genes within the same sample -keeping in mind a couple of reported biases like the size of the...
Forum: General 03-29-2012, 01:11 AM
Replies: 13
Views: 2,946
Posted By steven
Yes, i was referring to the actual google ranking...

Yes, i was referring to the actual google ranking (cf samanta's link), not to the original pagerank algorithm.
Forum: General 03-27-2012, 11:40 AM
Replies: 13
Views: 2,946
Posted By steven
Well, I have a couple of serious concerns...

Well, I have a couple of serious concerns regarding the google page rank as a metric for scientific papers/work in general. It is totally obscure, not disclosed, it can be -and is frequently-...
Forum: General 03-27-2012, 10:38 AM
Replies: 13
Views: 2,946
Posted By steven
Hi, I agree that there are a lot of issues...

Hi,

I agree that there are a lot of issues with the current "Impact Factor" criteria. This said I would not consider a Google rank as an acceptable way to assign a "value" to a scientific work...
Forum: Bioinformatics 03-27-2012, 07:33 AM
Replies: 2
Views: 896
Posted By steven
Just in case, don't forget to ask the author:...

Just in case, don't forget to ask the author: micha at sammeth dot net
Forum: Literature Watch 03-27-2012, 06:26 AM
Replies: 2
Views: 1,721
Posted By steven
Here is an "old" one: Comprehensive...

Here is an "old" one:
Comprehensive comparative analysis of strand-specific RNA sequencing methods
http://www.nature.com/nmeth/journal/v7/n9/abs/nmeth.1491.html
Forum: Bioinformatics 03-05-2012, 03:16 AM
Replies: 7
Views: 6,406
Posted By steven
I am confused about the terminology. What is your...

I am confused about the terminology. What is your data/experiment exactly? ESTs are not reliable and should not be used to infer expression values. If you are doing some Digital Gene Expression or...
Forum: Bioinformatics 03-02-2012, 03:10 AM
Replies: 21
Views: 8,634
Posted By steven
Thanks! Is the corresponding RNA-seq data...

Thanks! Is the corresponding RNA-seq data available too by any chance? :)
Forum: Bioinformatics 02-29-2012, 11:48 AM
Replies: 34
Views: 16,428
Posted By steven
Does a pilot have to be a mechanical engineer?

I strongly disagree with this.

Biology is an experimental science. The fact that you are a fan of biotechnology and computers -as many of us by the way- does not reduce biology to NGS data...
Forum: Bioinformatics 02-17-2012, 11:13 AM
Replies: 2
Views: 4,905
Posted By steven
I have seen a "Time series" option in Cufflinks...

I have seen a "Time series" option in Cufflinks (http://cufflinks.cbcb.umd.edu/manual.html) but I am not sure it is "appropriate". If there is something with edgeR or DESeq I am also interested.
Forum: Bioinformatics 02-17-2012, 11:02 AM
Replies: 6
Views: 3,619
Posted By steven
Why are DESeq and edgeR "far better" than...

Why are DESeq and edgeR "far better" than Cufflinks?

Do they take into account alternative splicing for instance?
I have strong concerns with the "exon union" approach.. adding read counts...
Forum: Complete Genomics 02-17-2012, 09:21 AM
Replies: 4
Views: 32,463
Posted By steven
I think that this is the transcription unit. As...

I think that this is the transcription unit. As said above, a CDS starts from the start codon and ends at the stop codon. UTRs are transcribed but not coding and therefore do not belong to the CDS.
...
Forum: General 02-08-2012, 08:46 AM
Replies: 3
Views: 1,669
Posted By steven
Recently a nice review...

Recently a nice review (http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html) was suggested to learn about genome assembly using De Bruijn graphs. You may want to look at transcriptome...
Forum: Bioinformatics 01-27-2012, 12:33 AM
Replies: 9
Views: 2,418
Posted By steven
Right, GMAP should do that. MapSplice too. ...

Right, GMAP should do that. MapSplice too.

GMAP:
-code (http://research-pub.gene.com/gmap/)
-ref1 (http://bioinformatics.oxfordjournals.org/content/21/9/1859.full)
-ref2...
Forum: Bioinformatics 01-27-2012, 12:25 AM
Replies: 13
Views: 4,570
Posted By steven
"samtools ...

"samtools (http://samtools.sourceforge.net/samtools.shtml)idxstats file.bam" seems to compute the number of reads per reference sequence -typically chromosomes. To get the number of reads per gene...
Forum: General 01-26-2012, 02:09 AM
Replies: 2
Views: 1,100
Posted By steven
Excellent summary indeed, clear and interesting...

Excellent summary indeed, clear and interesting pedagogy.
Forum: Bioinformatics 01-04-2012, 07:31 AM
Replies: 6
Views: 4,525
Posted By steven
Looking for co-expressed genes throughout time...

Looking for co-expressed genes throughout time points? I haven't seen much of this in NGS papers yet. What about a clustering approach? Maybe this thread...
Forum: Bioinformatics 12-19-2011, 09:30 AM
Replies: 2
Views: 1,481
Posted By steven
A genomic annotation can be manual, automated,...

A genomic annotation can be manual, automated, restrictive, exhaustive..
Refseq genes/transcripts usually require strong supporting evidence to be annotated by the NCBI, which explains why it is a...
Forum: Literature Watch 12-19-2011, 09:15 AM
Replies: 2
Views: 1,879
Posted By steven
It is very easy to get a picture of the trend...

It is very easy to get a picture of the trend using google scholar with the "Next Generation Sequencing" query and data limits....
Forum: General 12-01-2011, 12:55 AM
Replies: 26
Views: 13,318
Posted By steven
I joined that thread because the first post was a...

I joined that thread because the first post was a "stupid" question and those are often the most interesting ones.. Thanks Phillip and Tony for the details and explanations.
Forum: RNA Sequencing 12-01-2011, 12:40 AM
Replies: 2
Views: 1,480
Posted By steven
Here is an interesting comparative study from...

Here is an interesting comparative study from Levin et al:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005310/
Forum: Bioinformatics 11-25-2011, 09:20 AM
Replies: 4
Views: 1,425
Posted By steven
mhm.. if you consider the qPCR world (again) the...

mhm.. if you consider the qPCR world (again) the endogenous control classical approaches (like GeNorm (http://genomebiology.com/2002/3/7/research/0034/)and NormFinder...
Forum: RNA Sequencing 11-07-2011, 01:37 PM
Replies: 7
Views: 4,656
Posted By steven
That looks very exciting indeed! I was looking...

That looks very exciting indeed! I was looking forward to such a study..
Forum: Illumina/Solexa 11-07-2011, 01:28 PM
Replies: 1
Views: 5,240
Posted By steven
Did you try PubMed or Google Scholar...

Did you try PubMed or Google Scholar (http://scholar.google.es/scholar?q=%22HiSeq+2000%22&hl=en&btnG=Search&as_sdt=1%2C5&as_sdtp=on)?
For instance:
"Our results are based on analyses of a clinical...
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