User: TriS
TriS • 3.0k
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Posts by TriS
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... for DE transcripts keep the biological replicates separated, align them separately and then calculate DETs/DEGs.
for SNPs I'd suggest to do a similar approach. call SNPs per each replicate and keep those common across biological replicates. ...
written 18 days ago by
TriS • 3.0k
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Comment:
C: DESeq2 Heatmap issue
... figure margins too large
make the figure smaller and try again
png("qc-heatmap-samples.png", w=500, h=750) ...
written 22 days ago by
TriS • 3.0k
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33
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25k
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33
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... this should be posted as a new question since it's not specific for this tutorial.
anyhow..1) how does `head(rna)` look? 2) it seems you don't have a design matrix `d` 3) how many genes are in `rna`? ...
written 5 weeks ago by
TriS • 3.0k
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3
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... you don't need raw count values, you can use TPM and limma to get DEGs ...
written 7 weeks ago by
TriS • 3.0k
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294
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... it's a (partial) duplicate question from here:
https://www.biostars.org/p/248383/
here
https://www.biostars.org/p/8945/
see answers there.
also from Google:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/
https://www.bioconductor.org/help/workflows/rnaseqGene/
http://biocluster.ucr.edu/~r ...
written 7 weeks ago by
TriS • 3.0k
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2
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243
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... immunogenicity prediction is a very uncharted territory. that is, a potential antigenicity (or peptide recognition by the MHC) still does not tell you whether your lymphocytes have the receptor's repertoire (TCR or BCR) to recognize the peptide. this means that once you move into in vitro and in viv ...
written 7 weeks ago by
TriS • 3.0k
3
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1
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270
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1
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Answer:
A: CPM and FPKM value
... simple and to the point, thank you Google:
https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
...
written 7 weeks ago by
TriS • 3.0k
0
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2
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263
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2
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... are you trying to get the files that end with either bam.bai or .bai? if that's the case just grep out those with .bai....
how are your writing your workflow? unix shell? ...
written 8 weeks ago by
TriS • 3.0k
1
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4
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312
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4
answers
Answer:
A: Download data from TCGA
... easiest way:
1. go to cBioportal
2. click on the tumor type you want
3. on the right side click on "summary"
4. on the top of the page you have "download data"
..there you go ...
written 8 weeks ago by
TriS • 3.0k
1
vote
1
answer
177
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1
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... simplest ways:
go to cBioportal --> select your tumor type --> click on the right inside the link for "summary" --> on the top click the "download data"
1)
from here open the mutation data, skim for Her2 and get the corresponding patient IDs
then open the RNASeq data and select out th ...
written 8 weeks ago by
TriS • 3.0k
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