User: dvanic
dvanic • 70
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Posts by dvanic
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... Hi All
I was wondering - what is the most pain-free (or minimal pain) way of extracting a multiple sequence alignment to use with phyloCSF? (and, thanks, yes, I know there are other tools out there which are easier to use).
I am playing with new mm10 mouse transcripts (and, yes, I've looked at Gal ...
written 10 months ago by
dvanic • 70
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C: Splicing factor database
... Sorry if I wasn't clear (or I'm not finding the right link) - I need a list of things that work as splicing factors, not a tool to predict transcripts that could potentially be spliced... ????
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written 11 months ago by
dvanic • 70
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... Hi All,
I need a list of human/mouse splicing factors - what databases that are not abandonwhere do you use???
Thanks in advance!
PS I've found:
SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. which has 71 SF and was last updated in 2013 http://193.206.12 ...
written 11 months ago by
dvanic • 70
• updated 11 months ago by
gianluca.dellavedova • 50
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C: Soft Clipping
... Have you tested whether this works properly for paired-end reads?
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written 11 months ago by
dvanic • 70
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... See human and mouse.
...
written 11 months ago by
dvanic • 70
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... Have you seen http://genomebiology.com/2014/15/6/R86 by the same authors? I'm actually amazed that they got such "good" results with isoforms with their IVT data in the paper you discuss given how non-uniformly transcripts (i.e. isoforms) seem to be covered in the genome biology paper...
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written 12 months ago by
dvanic • 70
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... Nope, no source code or additional details!!! That's why it's so frustrating!!!
The problem is that their methods description is very confusing to me, AND they make a claim based on this approach that is very much critical for interpreting the results, especially the biology of their system. I've g ...
written 14 months ago by
dvanic • 70
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... I'm more trying to understand how they did it:
(1) ranking absolute gene expression for each microarray using Partek
(2) assigning a rank difference value for each gene using a MATLAB script
(3) calculating Spearman Rank Correlation Coefficients for each microarray comparison in Microsoft Excel
D ...
written 14 months ago by
dvanic • 70
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... I am trying to replicate the analysis conducted in Brennand et al (http://www.ncbi.nlm.nih.gov/pubmed/24686136) to cluster microarray expression data (or, in my case, RNA-seq data) with data available in the Allen Brain Atlas. I'm afraid their methods description is not clear enough for me to under ...
written 14 months ago by
dvanic • 70
• updated 14 months ago by
Michael Dondrup ♦ 33k
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