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Forum: Bioinformatics 07-25-2011, 08:52 AM
Replies: 5
Views: 39,338
Posted By altodor
So, from Ensembl or RefSeq we get translation...

So, from Ensembl or RefSeq we get translation start sites, don't we?

And a lot of bioconductor packages, when refering to TSS, actually give us translation start site, not transcription start...
Forum: Bioinformatics 07-17-2011, 06:42 AM
Replies: 5
Views: 39,338
Posted By altodor
transcription start sites (TSS)

Hi all!

I'm new to ChIPseq analysis and have a question regarding TSS.

I need to compare my ChIPseq regions against transcription start sites, human. Can I download TSS from Ensembl? Is...
Forum: Bioinformatics 06-16-2011, 12:18 AM
Replies: 3
Views: 2,033
Posted By altodor
And I have the same problem now. Does anyone...

And I have the same problem now.
Does anyone hear something from the authors or solve the problem?
Forum: Bioinformatics 06-07-2011, 12:30 AM
Replies: 7
Views: 7,801
Posted By altodor
Storey paper

There are excellent references in this paper:

http://www.nature.com/nbt/journal/v29/n4/full/nbt.1831.html?WT.ec_id=NBT-201104

John Storey

H. Craig Mak
Nature Biotechnology 29, 331333...
Forum: Bioinformatics 04-15-2011, 08:01 AM
Replies: 2
Views: 3,687
Posted By altodor
Thank you!

Thank you!
Forum: Bioinformatics 04-11-2011, 05:43 AM
Replies: 2
Views: 3,687
Posted By altodor
Question Cuffdiff and zero FPKM values give enormous log ratio

Hi all,
I'm new to RNA seq and I'm working with TopHat - Cufflinks - Cuffcompare - Cuffdiff pipeline.
I use Cufflinks without annotation and then Cuffcompare for two samples with annotation. I...
Forum: RNA Sequencing 02-16-2011, 12:04 AM
Replies: 3
Views: 5,540
Posted By altodor
Check reference.fa file. Mine was empty, may be...

Check reference.fa file. Mine was empty, may be that was the problem.
I built it manually using bowtie-inspect (there is such option, read bowtie-inspect help).
Now everything works.
Did it help...
Forum: Bioinformatics 02-16-2011, 12:02 AM
Replies: 2
Views: 1,704
Posted By altodor
Smile Problem solved

Hello, thank you!
It really worked with 8 threads. First problem was, that I ran 16 treads of tophat on 8 cores and they tried to read to the same folder.
Second problem, as appeared later, was the...
Forum: RNA Sequencing 01-26-2011, 12:04 PM
Replies: 0
Views: 1,743
Posted By altodor
tophat 1.2 multi thread mode error

Hi all,
running tophat 1.2 with 8 threads the following errors occur

srun: error: q44: tasks 0-6: Exited with exit code 1
And one thread continues running.

Also it seems like there is a...
Forum: Bioinformatics 01-26-2011, 12:03 PM
Replies: 2
Views: 1,704
Posted By altodor
Angry tophat 1.2 multi thread mode error

Hi all,
running tophat 1.2 with 8 threads the following errors occur

srun: error: q44: tasks 0-6: Exited with exit code 1
And one thread continues running.

Also it seems like there is a...
Forum: RNA Sequencing 01-12-2011, 06:26 AM
Replies: 3
Views: 5,540
Posted By altodor
Question TopHat - empty junction database

Hi all,

I ran TopHat, it aligned reads but couldn't find any junctions! So I received files with left-hand reads and right-hand reads (around 30 mln reads) , but the junction database is empy....
Forum: Introductions 01-10-2011, 10:17 AM
Replies: 0
Views: 829
Posted By altodor
Hello everybody!

Good luck to all of us in analyzing genome!
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