User: ag1805x
ag1805x • 110
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Posts by ag1805x
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Comment:
C: Questions about DAVID
... Which one is best suggested to annotate a set of up-regulated ges? ...
written 8 weeks ago by
ag1805x • 110
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... I am not sure about doing this on Python but guess we can get the nuber of reads in BAM file using [FASTQC][1].
[1]: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ...
written 10 weeks ago by
ag1805x • 110
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... Is it good to use DESeq2 normalized count for WGCNA. The counts obtained by `counts(dds, normalized=TRUE)` ...
written 3 months ago by
ag1805x • 110
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... I guess I need a bit more of help regarding this. I going through the graphs generated by the first three methods and something feels bad is going on; especially if you see box plot of normalized counts and density plot. Please see the attached files. The plots are similar for all of them so represe ...
written 4 months ago by
ag1805x • 110
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... So what's your opinion on using this. Something else I should try. Apart from this if I read correctly DESeq performs further cleaning. ...
written 4 months ago by
ag1805x • 110
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... I was experimenting with several like:
1) rowSums(count) > 0
2) rowMeans(count) > 1
3) rowSums(count>0)>10
4) apply(count, 1, function(x){all(x>0)})
The plots I provided above are from #4 and this is from DESeq2 manual (if I remember correctly). Initi ...
written 4 months ago by
ag1805x • 110
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... If you are looking for STRANDNESS then use infer_experiment.py from RseQC.
Refer http://rseqc.sourceforge.net/ & https://chipster.csc.fi/manual/library-type-summary.html ...
written 4 months ago by
ag1805x • 110
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... Why 10? Why not any other? ...
written 4 months ago by
ag1805x • 110
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... Thank you very much. This is really going to help me.
I more thing I need to clear. For box/violin plots do the first/third quartile or median for all the samples be at the same levels. For the same data set i was trying a different low count filter and after that I saw that the third quartile and ...
written 4 months ago by
ag1805x • 110
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... Any particular reason for choosing **10** and **300** in
> rowSums((counts(dds)) >= 10) >=300
I have seen several papers/tutorials using different strategy like rowSums>0 to filter low count genes, but I could never get the real reason. ...
written 4 months ago by
ag1805x • 110
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