Moderator: igor
igor ♦ 9.6k
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Posts by igor
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... Usually, only tumor cells should have copy number abnormalities. In panel B below (from [Patel et al][1]), you can see the topmost cluster has a flat copy number profile and contains the normal cells.
![enter image description here][2]
[1]: https://dx.doi.org/10.1126%2Fscience.1254257
[2]: ht ...
written 1 day ago by
igor ♦ 9.6k
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... With some caveats (see [this Twitter thread][1] or [the corresponding blog post][2]).
[1]: https://twitter.com/lpachter/status/1223745770240655361
[2]: https://fromsystosys.netlify.com/2020/01/31/comparing-ensembl-gtf-and-cdna/ ...
written 1 day ago by
igor ♦ 9.6k
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... If you are interested, there are a few other alternatives discussed here: https://www.biostars.org/p/274762/ ...
written 1 day ago by
igor ♦ 9.6k
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... It will depend on your tumor type. Some are easier to differentiate than others.
You don't necessarily need to identify tumor cells to call CNVs. In fact, you could call CNVs to identify tumor cells. ...
written 2 days ago by
igor ♦ 9.6k
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... > Is it possible to use GATK (Broad Institute) to analyse this kind of
> data (even though it was not properly created for RNAseq analysis)?
There is a GATK workflow specifically for RNA-seq: https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-In ...
written 3 days ago by
igor ♦ 9.6k
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... There are many vignettes that show this just to say that it is possible. As you already mentioned, there are potential problems with this approach. This may explain why most publications do not take this approach. ...
written 3 days ago by
igor ♦ 9.6k
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Comment:
C: Bioinformatics Server on AWS
... You should find the optimal solution to your problem. If you don't know what services AWS provides, then how do you know you should be using AWS? ...
written 6 days ago by
igor ♦ 9.6k
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... There have been a number of free data storage solutions that popped up in the last few years, such as Figshare, OSF, and Zenodo. You can even use GitHub if the files are under 100 MB. I think there are others that I am forgetting. Is there a comparison available somewhere? Nature Scientific Data has ...
written 6 days ago by
igor ♦ 9.6k
• updated
6 days ago by
Alex Reynolds ♦ 29k
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... I am not sure you need a package. Just use `fisher.test()`. ...
written 6 days ago by
igor ♦ 9.6k
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... That's a good point. I don't know if the distinction is always clear. Sometimes people who are helping out of goodness of their heart are treated as a core facility. ...
written 11 days ago by
igor ♦ 9.6k
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