Moderator: igor
igor ♦ 7.6k
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Posts by igor
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... You should consider changing your question to the actual problem you are having, which is "find the genes that may causes the disease". GATK helps you get mutations, but it will not help you with understanding them. ...
written 5 days ago by
igor ♦ 7.6k
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... What if you try to align R1 or R2 independently? There might be an issue with insert sizes. ...
written 8 days ago by
igor ♦ 7.6k
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... You probably want to use a table of expression values, not stats. ...
written 13 days ago by
igor ♦ 7.6k
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1.2k
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... Yes, link rot is a problem. Luckily, Google still exists. ...
written 14 days ago by
igor ♦ 7.6k
2
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93
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Answer:
A: Binary mutation data format
... I think the matrix you are looking for can be found at [Xena gene level non-silent mutations][1].
[1]: https://xenabrowser.net/datapages/?dataset=mc3.v0.2.8.PUBLIC.nonsilentGene.xena&host=https%3A%2F%2Fpancanatlas.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 ...
written 15 days ago by
igor ♦ 7.6k
0
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... I edited the statement to make it more clear. I originally meant that all genes (as opposed to all cells) are scaled, but I can see how it can be interpreted in a different way. ...
written 15 days ago by
igor ♦ 7.6k
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... Don't you have to be invited for a review? Or are we talking about different reviews? ...
written 16 days ago by
igor ♦ 7.6k
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... Is it politically correct to write a sole author paper while in someone else's lab?
In this particular case, the author is relatively new to bioinformatics. It sounds like he does not have any publications (even middle author). How do you get a review in that position? ...
written 16 days ago by
igor ♦ 7.6k
3
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... If you are interested in specific genes, you would probably want to use gnomAD exomes, not genomes. It's based on more samples and the file is substantially smaller. ...
written 17 days ago by
igor ♦ 7.6k
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... > someone's interest organism is might not be covered by these tools
There are many tools that will work for any organism.
> I am interested in figuring out this stuff myself
If you have already found some tools, check their source code, which should be available for most of them.
...
written 17 days ago by
igor ♦ 7.6k
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