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Recent Replies
Comment: Finding a known duplication mutation in a VCF file
by
Pierre Lindenbaum
146k
> The VCF is the only input file I got.
so the only tool I know is `bcftools roh` but IMHO, you cannot check if there is a true positive w…
Comment: Finding a known duplication mutation in a VCF file
by
langzvi
•
0
It's a gene with length of 35,548 nt according to NCBI, so it's pretty big. So, you suggest converting the VCF to a BAM file?
The VCF is th…
Comment: Searching for RNA-seq melanoma samples in TCGA or cBioPortal
by
JACKY
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I want processed SKCM data (preferably counts, but normalized data would also work.. like RPKM or TPM). And for the same samples, I want t…
Comment: Finding a known duplication mutation in a VCF file
by
Pierre Lindenbaum
146k
is it a small duplication or a SV/SNV ? better than a vcf would be to call the vCNV/SV from a bam with manta/smoove/delly etc....
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★
4.8k
> The DESeq2 vignette offers a pretty comprehensive run-down of the entire process, starting with read quantification import and listing th…
Comment: Survival analysis based on a set of genes for TCGA data
by
yussufhajjaj93
•
0
Hi Hamid, thank you so much for the tutorial! But I wanted to ask if there a simple way to classify the data into quartiles or tertiles usi…
Comment: Getting the best of RNA-Seq
by
GenoMax
117k
> one being that not DE genes are expressed, and the other giving
> rational but inaccurate DE expression
Sounds like your experiment is n…
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★
4.8k
> What do you mean by "rational, but inaccurate DE expression"? How do you gauge both rationality as well as accuracy of your results?
B…
Comment: Getting the best of RNA-Seq
by
Antonio R. Franco
★
4.8k
This is the actual problem. If you are using as reference for the mapping a fasta file containing isoforms, your analysis should be address…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
Friederike
8.4k
If these are unsorted files, why would you need the last read? Couldn't you pick a random read or the first one?
Comment: Getting the best of RNA-Seq
by
Friederike
8.4k
>To mention, I started to use Kallisto and DESeq2 to see that after importing the data with the tximport package using the txOut = FALSE or…
Comment: Searching for RNA-seq melanoma samples in TCGA or cBioPortal
by
Friederike
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Can you specify a bit more what the end goal is? I.e. what type of data (processed, raw, ...) would you like to download and what would you…
Comment: Align short sequence against ONT reads
by
Friederike
8.4k
Are the long reads very different from each other (e.g. covering different regions of the genome) or do they all represent the same (more o…
Answer: Clustered, annotated dotplot to scRNA-Seq data
by
Friederike
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The [`dittoSeq`](https://github.com/dtm2451/DittoSeq) package also offers a [`dotPlot` function](http://bioconductor.org/packages/release/b…
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