User: dsull
dsull • 1.7k
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Name: Delaney Sullivan
Currently at UCLA (formerly at Stanford)
Posts by dsull
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... Do you really need to use alignment for bulk RNA-seq? Why not use pseudoalignment? Less memory and computing requirements. ...
written 12 days ago by
dsull • 1.7k
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... You can also just normalize TPMs using DESeq size factors. I don't see anything wrong with doing so. ...
written 13 days ago by
dsull • 1.7k
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Comment:
C: GSEA for scRNA-seq
... Also, I just realized you posted a near-identical question here: https://www.biostars.org/p/482173/
The response there already answers your question. ...
written 17 days ago by
dsull • 1.7k
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Comment:
C: GSEA for scRNA-seq
... "For GSEA, I want to use only DEGs with adj p-value < 0.05"
You can't do that. For GSEA, you have to use all genes (supplied with their expression data), not just the DEGs.
You'd have to use pathway overrepresentation analysis (e.g. as typically done in gene ontology enrichment) if you want to ...
written 17 days ago by
dsull • 1.7k
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... Correct; kallisto and salmon quantification are much better. See:
https://twitter.com/lpachter/status/1060597618479267840 ...
written 20 days ago by
dsull • 1.7k
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... It's actually more accurate to get gene-level expression from transcript-level estimates.
Many papers have been written on this e.g.:
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences (this is the tximport paper)
...
written 6 weeks ago by
dsull • 1.7k
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... I have no idea what you're doing for your reference transcriptome (language is very unclear).
But to do gene-level analysis with DESeq2, you have to summarize the transcript-level estimates to gene-level (see: tximport).
If you want to do transcript-level differential expression analysis, I'd reco ...
written 7 weeks ago by
dsull • 1.7k
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... Why not just convert FPKMs to TPMs? ...
written 10 weeks ago by
dsull • 1.7k
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... Loom files store data matrices in single-cell RNA-seq and is what velocyto works with to do RNA velocity.
The loom file is here: http://pklab.med.harvard.edu/velocyto/hgForebrainGlut/hgForebrainGlut.loom
Basically, this file was made by different pipeline in a previous study (see the paper: RNA ve ...
written 11 weeks ago by
dsull • 1.7k
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... Thanks! Here's something that should work for generating the index (this is what worked on my end). It involves installing/upgrading kb-python's development release.
```
pip install git+https://github.com/pachterlab/kb_python@devel --upgrade
kb ref -i mouse_velocity_index.idx -g mouse_velocity_t2g ...
written 11 weeks ago by
dsull • 1.7k
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