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Search: Posts Made By: Thomas Doktor
Forum: Bioinformatics 08-16-2017, 02:16 AM
Replies: 7
Views: 2,109
Posted By Thomas Doktor
Looks to me like an error in the Ensembl...

Looks to me like an error in the Ensembl annotation, transcript ENST00000639671 is misannotated as being a transcript produced by the TOM1L1 gene (TOM1L1-224), when it is in fact a COX11 derived...
Forum: Bioinformatics 08-13-2013, 10:55 AM
Replies: 3
Views: 1,426
Posted By Thomas Doktor
I would recommend trying DEXSeq for your...

I would recommend trying DEXSeq for your analysis. It is based on DESeq and can relate alternative exons to isoforms.
Forum: Bioinformatics 12-11-2012, 07:47 AM
Replies: 3
Views: 9,734
Posted By Thomas Doktor
You should filter according to the FDR value and...

You should filter according to the FDR value and not the raw p-value, that's why you are seeing more differentially expressed genes using your own function compared to the built-in in edgeR. Why not...
Forum: Bioinformatics 12-04-2012, 07:55 AM
Replies: 9
Views: 1,864
Posted By Thomas Doktor
GOrilla links to REVIGO which I think will do...

GOrilla links to REVIGO which I think will do what you are looking for:
http://revigo.irb.hr/
Forum: RNA Sequencing 11-19-2012, 05:00 AM
Replies: 67
Views: 74,265
Posted By Thomas Doktor
Could you elaborate a bit on what kind of...

Could you elaborate a bit on what kind of tweaking you have done with the cufflinks options sdriscoll?
Forum: Bioinformatics 08-08-2012, 04:04 AM
Replies: 5
Views: 24,782
Posted By Thomas Doktor
There's a conversion tool at the David website:...

There's a conversion tool at the David website: http://david.abcc.ncifcrf.gov/conversion.jsp
Forum: Bioinformatics 03-28-2012, 02:50 AM
Replies: 33
Views: 37,303
Posted By Thomas Doktor
You could do it with merge:

You could do it with merge:
Forum: RNA Sequencing 03-15-2012, 08:20 AM
Replies: 6
Views: 9,917
Posted By Thomas Doktor
You're right, they were just well hidden :) (and...

You're right, they were just well hidden :) (and I never had use for anything other than the default).
Forum: RNA Sequencing 03-15-2012, 05:18 AM
Replies: 6
Views: 9,917
Posted By Thomas Doktor
TopHat doesn't have those options, are you sure...

TopHat doesn't have those options, are you sure you're not thinking of Cufflinks?
For the scriptseq v2 kit I would use the fr-secondstrand librarytype since the first read will be the left-most in...
Forum: Bioinformatics 02-02-2012, 04:11 AM
Replies: 5
Views: 4,328
Posted By Thomas Doktor
Cuffdiff supports replicates but does not handle...

Cuffdiff supports replicates but does not handle paired replicates to my knowledge.

Btw, I would recommend using DESeq instead of DEGseq, the spelling is similar but the internal statistical...
Forum: Bioinformatics 11-24-2011, 06:11 AM
Replies: 13
Views: 4,424
Posted By Thomas Doktor
Where do you see the release of version 1.3.1 and...

Where do you see the release of version 1.3.1 and 1.3.3? They are downloadable from the site, but nothing about them is mentioned on the TopHat site.
Forum: Bioinformatics 10-14-2011, 05:41 AM
Replies: 6
Views: 3,909
Posted By Thomas Doktor
Did you check that the...

Did you check that the Homo_Sapiens_Ensembl_GRCh37.tar.gz contained a gtf file with "chr1,chr2,.." type identifiers instead of the "1,2,..." type?

You can convert it this way:
cat genes.gtf | awk...
Forum: Bioinformatics 10-14-2011, 04:50 AM
Replies: 1
Views: 1,806
Posted By Thomas Doktor
You have to install R2.14 in order to install...

You have to install R2.14 in order to install Bioconductor 2.9 which contains Biobase 2.13.10. Note that R2.14 is alpha and Bioconductor 2.9 is in development.
Forum: Bioinformatics 08-08-2011, 05:37 AM
Replies: 5
Views: 3,747
Posted By Thomas Doktor
How do you know they're not responding to the -p...

How do you know they're not responding to the -p option?
Do they output an error message or are you checking the use of multiple CPU's by the top command? What was the exact command you used?
Forum: Bioinformatics 05-30-2011, 06:27 AM
Replies: 12
Views: 23,415
Posted By Thomas Doktor
This might explain it:

This might explain it:
Forum: Bioinformatics 03-17-2011, 07:36 PM
Replies: 5
Views: 5,352
Posted By Thomas Doktor
Look here for a solution to "-lpthread":...

Look here for a solution to "-lpthread": http://www.justlinux.com/forum/showthread.php?t=126349

"-lz" is the zlib which you have installed. Is the Mosaik buildprocess looking in the right folder?...
Forum: Bioinformatics 03-03-2011, 05:04 AM
Replies: 12
Views: 7,729
Posted By Thomas Doktor
My guess is that it's not unpaired mapped reads,...

My guess is that it's not unpaired mapped reads, but simply unpaired reads. Both reads are present in the SAM file, even if only one of them is actually mapped. Picard is just telling you that it...
Forum: Bioinformatics 02-24-2011, 04:09 AM
Replies: 4
Views: 3,831
Posted By Thomas Doktor
Can you give an example of the intended output? ...

Can you give an example of the intended output?

I'm thinking you would like this:
File 1:
E.coli ---MGKALVIVESPAKAKTINKYLGSD-----------YVVKSSVGHIRDLPTSGSAAKK
E.coli ---ALISLILIASLILILAISLA
...
Forum: Bioinformatics 02-23-2011, 10:57 AM
Replies: 12
Views: 7,729
Posted By Thomas Doktor
Thanks for clearing that up.

Thanks for clearing that up.
Forum: Bioinformatics 02-23-2011, 04:57 AM
Replies: 12
Views: 7,729
Posted By Thomas Doktor
By collapsing I mean removing all but a single of...

By collapsing I mean removing all but a single of the duplicate reads. My question is if picard tools marks all the duplicate reads as duplicates or keeps one read as the "original"?
Forum: Bioinformatics 02-22-2011, 04:49 AM
Replies: 12
Views: 7,729
Posted By Thomas Doktor
What if you wanted to collapse all PCR duplicates...

What if you wanted to collapse all PCR duplicates into a single read? Doesn't picard tools simply flag them as PCR duplicates and if you remove them you will lose that read position completely?
Or...
Forum: Bioinformatics 02-21-2011, 11:08 AM
Replies: 12
Views: 7,729
Posted By Thomas Doktor
I would say that PCR duplicates in SE sequencing...

I would say that PCR duplicates in SE sequencing can appear as having different end coordinates and different sequences because the PCR process itself can induce errors and the sequencing can...
Forum: Bioinformatics 01-06-2011, 10:06 AM
Replies: 23
Views: 30,672
Posted By Thomas Doktor
And you are sure the mm9.ensembl.gtf is the...

And you are sure the mm9.ensembl.gtf is the corrected one?
Forum: Bioinformatics 01-06-2011, 10:02 AM
Replies: 23
Views: 30,672
Posted By Thomas Doktor
TopHat did not produce any errors here. What...

TopHat did not produce any errors here. What commands did you use?
Forum: Bioinformatics 01-06-2011, 09:18 AM
Replies: 23
Views: 30,672
Posted By Thomas Doktor
There seems to be an error (possibly a...

There seems to be an error (possibly a duplication) with the entries for the ENSMUST00000127664 transcript in the Ensembl mm9 gtf file.

You can correct your Ensembl file this way (I have...
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