User: igor
igor • 4.6k
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Posts by igor
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... They are from different cell types. ...
written 3 days ago by
igor • 4.6k
1
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... There should be a description somewhere, but I am not sure where. That would be a question for ENCODE.
Regarding bins, most operations in Hi-C are on a bin level since it's not possible to get single-base resolution. This means the genome is broken into bins/regions/windows (usually 10-40 kb).
A g ...
written 6 days ago by
igor • 4.6k
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Answer:
A: FPKM threshold and filter
... You can try to use a zFPKM transform to define expressed genes: https://bioconductor.org/packages/devel/bioc/vignettes/zFPKM/inst/doc/zFPKM.html
> we provide a novel normalization metric, zFPKM, that identifies the
> threshold between active and background gene expression; and we show
> th ...
written 8 days ago by
igor • 4.6k
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... Can you clarify "looked like a lot of PCR artifacts from the library prep"? Do you mean you have a lot of duplicates or is it something else? Is it just in one group and not the other? ...
written 13 days ago by
igor • 4.6k
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Comment:
C: RNA-seq rRNA contamination
... Yes, that is essentially the first method I mentioned. ...
written 13 days ago by
igor • 4.6k
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4
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... You can calculate the overlap by comparing the read length to the fragment/insert size. There are a few ways to do that. See this previous discussion: https://www.biostars.org/p/65262/ ...
written 13 days ago by
igor • 4.6k
0
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1
answer
715
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Comment:
C: heatmap using FPKM values
... > the sequencing facility has given me cuffdiff results so that is what
> i have to work with
If you already have the Cuffdiff results, then you already have differentially expressed genes. ...
written 14 days ago by
igor • 4.6k
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7
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Answer:
A: spreadsheet tools alternative
... A lean and simple (only 218 bytes!) spreadsheet app: http://xem.github.io/sheet/
Free, open source, and no extra crud to mess up dates!
...
written 18 days ago by
igor • 4.6k
1
vote
7
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265
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7
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Comment:
C: spreadsheet tools alternative
... This is not a fair question. You are saying it's too hard to adjust some settings in Excel. Learning how to use a completely new software tool will not be easier. ...
written 18 days ago by
igor • 4.6k
0
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... I don't know if there is a package for that, but you can use ggplot `geom_jitter` to do something similar. It's not the same, but it will let you see the distribution of the individual values.
![enter image description here][1]
[1]: http://ggplot2.tidyverse.org/reference/geom_jitter-4.png ...
written 18 days ago by
igor • 4.6k
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