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User: dsull

gravatar for dsull
dsull • 1.7k
Reputation:
1,720
Status:
Trusted
Location:
UCLA
Last seen:
6 hours ago
Joined:
4 years, 5 months ago
Email:
d****@stanford.edu

Name: Delaney Sullivan

Currently at UCLA (formerly at Stanford)

Posts by dsull

<prev • 171 results • page 1 of 18 • next >
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Comment: C: Hardware requirements for bowtie2/STAR RNA-seq alignment
... 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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Comment: C: In-sample and across samples normalized expression
... 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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Comment: C: Differential Expression Analysis with Salmon vs Genomic Aligners Like Star
... 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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Comment: C: Differential analysis isoform level or gene level ?
... 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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Comment: C: Differential analysis isoform level or gene level ?
... 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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Comment: C: Normalize FPKM values for cross-sample comparisons?
... Why not just convert FPKMs to TPMs? ...
written 10 weeks ago by dsull • 1.7k
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Answer: A: Kallisto single cell velocity tutorial question
... 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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Comment: C: Kallisto Bustools Single Cell Velocity Issue: capture and count not working as e
... 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

Latest awards to dsull

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 11 weeks ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 3 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
Appreciated 4 months ago, created a post with more than 5 votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
Scholar 7 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 7 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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Scholar 9 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 11 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
Scholar 12 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 12 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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