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Recent Replies
Comment: RNA-seq analysis
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Gordon Smyth
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Yes, the code I gave you will work on any BAM file. In general, strand information is used only when assigning read alignments to genes, no…
Comment: RNA-seq analysis
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SEJAL
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Will it work on BAM files that I obtained from HISAT2 with default option of strandedness, i.e. unstranded?
Or STAR aligned BAM files (whic…
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Hi Pierre,
I'm new to the GFF format and learning from your post. I wonder if I understand correctly, that each CDS regions doesn't need t…
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`vg surject` doesn't do a full realignment of the read against the linear reference. In general, it tries to preserve as much of the graph …
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Finding recent **public** human tumor sequence data (and VCF) is going to be rare because of patient privacy concerns. You could sign up an…
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Thanks for the historical blah! Happy to be reader #14.
Hopefully the past 20 years have demonstrated that a statement like "Figure 2 show…
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Can you show the `colData` data? It’s important that `colData$sampleID` is identical to `rownames(colData)` and to the sample names in `jun…
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thank you for the resources, will try and update
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On the subject of DE, way back in the days of microarrays, this pooling/ sub-pooling issue was big. Gary Churchill warned everybody here
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When you save a plot in a vector format such as SVG or PDF, there will be objects that can be moved around as units. You can literally drag…
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Here's the one-liner for Medhat's useful command:
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yes, you can try [this][1]
[1]: https://stuartlab.org/signac/reference/callpeaks
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1769mkc
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Naive question So that is the only information I would need for mac2 input?
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What species are you working on and which cell types are you interesting in ?
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You can call peaks again from the fragments file using Macs2 like they did in the paper. Then you can add your `peaks x cells` matrix as a …
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