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Comment: ONT Live-Basecalling Issue?
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LauferVA
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Yikes. This is scary. I'd definitely contact ONT.
No other error messages? Regarding this:
> What is the issue here? And is a potential s…
Answer: Using DEXseq on kallisto tsv outputs ?
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Gordon Smyth
★
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Inputting transcript (RNA isoform) quantifications from kallisto into tools like DEXSeq that are designed for exons is not ideal because th…
Comment: ChIP-seq gene blacklist for Rattus norvegicus
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GenoMax
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https://kilthub.cmu.edu/articles/dataset/Alternate_gene_annotations_for_rat_macaque_and_marmoset_for_single_cell_RNA_and_ATAC_analyses/2117…
Comment: ChIP-seq gene blacklist for Rattus norvegicus
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RD
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Were you able to find the list of regions?
Thank you!
Comment: Extracting Variant Sequences from 1000 Genomes VCF File and Mapping to Canonical
by
cmdcolin
★
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doesn't solve your problem exactly but I stumbled on this blog post awhile back
https://kalis.louisaslett.com/articles/lct_example.html#re…
Answer: Extract length of sample sequence from vcf
by
cmdcolin
★
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Not sure if it helps but I saw this impressive one-liner in a blog post that 'reconstructs the sequence for the 1000 genomes samples'
http…
Comment: RNA-seq, three comparisons - stick to one linear model, or use separate models?
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Thank you @ATpoint
Comment: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an
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Hao
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it's a bioarxiv so I didn't provide the link. Anyway, link added and I changed the language.
Comment: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an
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Please edit the answer above and provide a link (either PubMed or direct journal) for the paper. Just saying you did "X" is not providing a…
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> What is the best trade off in this scenario?
As noted earlier, this data is ~ 15 yr old at this point i.e. from the dawn of NGS tech. It…
Answer: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an
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Sure. In [one of our preprints][1], we did sort of a similar thing on cells from different time points.
[1]: https://www.biorxiv.org/c…
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You could also use an ORF finder like transdecoder or prodigal as an additional check. Many lncRNAs might have very short ORFs, but are unl…
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Both TPM and FPKM will normalize to the so-called "library size", which is how many mapped reads are in each sample. So, that is not what c…
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make sure the variants are normalized and properly decomposed, also maybe show that VCF row as well,
This example you gave seems to show…
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