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Recent Replies
Comment: Viral genes not showing up in combined mouse+virus alignment
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I figured it out! The GTF.featureType uses 'exon' by default which is present in the mouse GTF but the viral GTF file has no exon feature n…
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This vignette will help you. [https://satijalab.org/seurat/articles/seurat5_cell_cycle_vignette][1]
[1]: https://satijalab.org/seurat/…
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Yep gave that a go and proceeding with the analysis. Thanks again.
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Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …
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Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
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Here is the output with the "-v 4" flag (not showing all the @SQ comments) :
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There is a ready-made package for samtools, simply do
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Use option `-v` with value of 4 or above to help diagnose the issue:
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Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
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Thank you, I really appreciate your insight! I will look into the dropouts I have.
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Are you analysing RNA or DNA heteroplasmy levels?
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Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
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edgeR *is* an NB-GLM.
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Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
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its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
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