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Search: Posts Made By: feralBiologist
Forum: Bioinformatics 06-07-2016, 08:39 AM
Replies: 5
Views: 2,973
Posted By feralBiologist
I tried using "--compliant" and "--centre XX"...

I tried using "--compliant" and "--centre XX" alone and in combination and it didn't work.
Forum: Bioinformatics 02-11-2016, 01:50 AM
Replies: 0
Views: 1,677
Posted By feralBiologist
Comparative bacterial genomics on groups of samples

Here is my project:

- I have a group X of unknown strains of species A taken from, say, the oral cavities of a group of people. Each individual gives rise to a single sample. The bacterial species...
Forum: Bioinformatics 02-21-2015, 08:22 PM
Replies: 3
Views: 2,745
Posted By feralBiologist
I don't have a clear idea about the read groups -...

I don't have a clear idea about the read groups - my hunch is that I need to worry about them only if I have multiplexed samples in the same BAM. My BAMs contain single samples - what is the...
Forum: Bioinformatics 02-21-2015, 05:59 PM
Replies: 3
Views: 2,745
Posted By feralBiologist
How to use AddOrReplaceReadGroups.jar with Tophat2 BAMs?

My travails started when I tried to produce mapping stats (exons, introns, intergenic regions) for RNA-Seq samples aligned with Tophat2 and Ensembl GTF files. For a number of reasons RNA-SeQC seems...
Forum: Bioinformatics 02-20-2015, 01:42 PM
Replies: 15
Views: 10,921
Posted By feralBiologist
Unfortunately, I did quite a bit of work already...

Unfortunately, I did quite a bit of work already using the Ensembl GTF - I would have to start afresh and discard all the work done so far as I can't be certain that the Ensembl version I am using...
Forum: Bioinformatics 02-20-2015, 10:03 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
If anyone is interested - here is the GTF I used...

If anyone is interested - here is the GTF I used (http://bit.ly/1BvzUde), the refFlat produced (http://bit.ly/1CVyVAZ), and here are the command line arguments I used for CollectRnaSeqMetrics:
...
Forum: Bioinformatics 02-20-2015, 06:43 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
I ran into troubles again. I was able to run...

I ran into troubles again. I was able to run gtfToGenePred and it produced a refFlat file from the Ensembl GTF file. However, when I tried using it with Picard's CollectRnaSeqMetrics I got
...
Forum: Bioinformatics 02-19-2015, 05:23 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
Thanks - I think it's robots.txt that UCSC put...

Thanks - I think it's robots.txt that UCSC put which prevented Google from displaying that site.
Forum: Bioinformatics 02-19-2015, 05:19 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
I am on MacOS X. Actually, I could not find a...

I am on MacOS X. Actually, I could not find a proper download page - just opening one of the Google search results ended up automatically downloading the binary.
Forum: Bioinformatics 02-19-2015, 04:43 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
Thanks. I tried it but it does not seem to work: ...

Thanks. I tried it but it does not seem to work:

localhost:Downloads nnikolo$ ls -lt gtf*
-rwxr-xr-x@ 1 nnikolo staff 12944032 19 Feb 12:18 gtfToGenePred
localhost:Downloads nnikolo$...
Forum: Bioinformatics 02-19-2015, 03:49 AM
Replies: 4
Views: 3,014
Posted By feralBiologist
Thanks, Michael. I am not sure RSeQC would do the...

Thanks, Michael. I am not sure RSeQC would do the job as, to quote, .
Forum: Bioinformatics 02-19-2015, 03:42 AM
Replies: 15
Views: 10,921
Posted By feralBiologist
How to convert GTF to RefFlat?

My use case is as follows:

I have aligned RNA-Seq data using tophat2 and a GTF file I got from Ensembl. Now I would like to produce alignment stats (number of reads mapping to exons, introns,...
Forum: Bioinformatics 02-19-2015, 03:33 AM
Replies: 4
Views: 3,014
Posted By feralBiologist
I just googled it but it seems that...

I just googled it but it seems that CollectRnaSeqMetrics does not take as input GTF files. It requires RefFlat files. I am googling at the moment but cannot find documentation on how to convert gtf...
Forum: Bioinformatics 02-17-2015, 02:38 PM
Replies: 4
Views: 3,014
Posted By feralBiologist
Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?

I aligned RNA-Seq data to a genome using tophat2. Now I have the bam file and I am looking for a straight-forward way to produce mapping statistics - how many reads map onto exons, introns and...
Forum: Bioinformatics 02-15-2015, 11:17 AM
Replies: 9
Views: 4,693
Posted By feralBiologist
I found the answer to this on CrossValidated...

I found the answer to this on CrossValidated (http://stats.stackexchange.com/questions/80534/what-are-the-units-in-this-pca-biplot): it seems the units denote the raw component scores. As the...
Forum: Bioinformatics 02-15-2015, 09:52 AM
Replies: 9
Views: 4,693
Posted By feralBiologist
Yes, I know these are the principal components....

Yes, I know these are the principal components. It is just that DESeq2 prints units on these axes (you can check the link to the plot in my first post) and I could not make any sense of these. I also...
Forum: Bioinformatics 02-15-2015, 06:25 AM
Replies: 9
Views: 4,693
Posted By feralBiologist
Thanks for your reply! So you are saying the...

Thanks for your reply! So you are saying the units printed on the x/y axes have no meaning? Do you know how can I edit the code to remove them?
Forum: Bioinformatics 02-14-2015, 04:26 PM
Replies: 9
Views: 4,693
Posted By feralBiologist
Interpreting a PCA plot produced with DESeq2

I've used DESeq2 to analyse a few RNA-Seq samples. I followed pretty closely the manual and using the following code

vsd <- varianceStabilizingTransformation(dds)
data <- plotPCA(vsd,...
Forum: Bioinformatics 08-31-2014, 06:35 AM
Replies: 2
Views: 2,519
Posted By feralBiologist
RNA expression - reads mapping outside of the annotated regions of the genome

I have data from an experiment which is looking into differential expression of small RNA. It seems that a fraction of the reads are mapped outside of the annotated regions of the mouse genome (as...
Forum: Bioinformatics 08-19-2014, 02:49 PM
Replies: 9
Views: 3,270
Posted By feralBiologist
Thanks for your response but it still does not...

Thanks for your response but it still does not clarify the question I asked. OK, let's drop "normalisation" as it is a confusing term. What I really wanted to know is "How do you come from raw counts...
Forum: Bioinformatics 08-19-2014, 09:14 AM
Replies: 9
Views: 3,270
Posted By feralBiologist
Now I am confused again. And maybe I am not the...

Now I am confused again. And maybe I am not the only one as the response by James MacDonald in the bioconductor thread indicates. I believe this confusion is due to the fact that "normalization" in...
Forum: Bioinformatics 08-18-2014, 03:03 AM
Replies: 9
Views: 3,270
Posted By feralBiologist
You are right - and I once again thank you for...

You are right - and I once again thank you for this. I will not post edgeR questions to seqanswers anymore. In the past I have used seqanswers a lot more often than I have used bioconductor (and not...
Forum: Bioinformatics 08-16-2014, 08:17 AM
Replies: 9
Views: 3,270
Posted By feralBiologist
dpryan, I see your point (and appreciate the help...

dpryan, I see your point (and appreciate the help you have generously given on so many occasions) but the reason for cross-posting is that not everyone is following all the forums. In this case...
Forum: Bioinformatics 08-16-2014, 03:52 AM
Replies: 9
Views: 3,270
Posted By feralBiologist
the counts reported by edgeR are not normalized

This is the kind response by James MacDonald which I got in the Bioconductor list:

https://stat.ethz.ch/pipermail/bioconductor/2014-August/061055.html

In short, the scores reported in...
Forum: Bioinformatics 08-15-2014, 07:32 AM
Replies: 9
Views: 3,270
Posted By feralBiologist
zero rna-seq values AFTER normalisation in edgeR

I am using edgeR to analyze RNA-Seq data. This is my script:


library("edgeR")
#############################
#read in metadata & DGE
#############################
composite_samples <-...
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