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Recent Replies
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
★
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> 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
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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
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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
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Antonio R. Franco
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> 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
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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?
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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
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>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…
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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…
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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…
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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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lieven.sterck
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Hello https://www.biostars.org/u/110969/,
Welcome to the forum!
Please use the formatting bar (especially the `code` option) to present y…
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The size is 24661059 and I waited aroun 10 mins
Comment: Getting the best of RNA-Seq
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ATpoint
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It is unclear to me what the question is. Do you want gene-level or transcript-level analysis? From what I know gene level analysis does no…
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