User: Lior Pachter
Lior Pachter • 460
- Reputation:
- 460
- Status:
- Trusted
- Location:
- United States
- Website:
- https://pachterlab.git...
- Twitter:
- @lpachter
- Last seen:
- 1 week, 2 days ago
- Joined:
- 4 years, 2 months ago
- Email:
- l*******@caltech.edu
Posts by Lior Pachter
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Comment:
C: RNA velocity on 5' 10x data?
... FYI you can now run RNA velocity with three commands:
$ pip install kb-python
$ kb ref -d linnarsson -i idx.idx -t t2g.txt -c1 t2c_cDNA.txt -c2 t2c_intron.txt
$ kb count --lamanno --filter --h5ad -i idx.idx -g t2g.txt -x 10xv2 -c1 t2c_cDNA.txt -c2 t2c_intron.txt R1.fastq.gz R2.fastq.gz
See https:/ ...
written 9 days ago by
Lior Pachter • 460
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... You should modify your transcriptome to include both haplotypes for the gene. ...
written 6 weeks ago by
Lior Pachter • 460
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... Regarding the pros and cons of the programs, you might find this article useful:
[https://www.nature.com/articles/s41598-017-01617-3][1]
It finds that kallisto and Salmon produce near identical results, and that STAR (with HTseq for producing gene counts) is less accurate (due to some of the reason ...
written 7 weeks ago by
Lior Pachter • 460
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... Unfortunately it's not that simple- bulk RNA-seq has reads from across transcripts and so quantification requires normalization by length. Having said that, if you are only interested in producing transcript compatibility counts then yes, this index can be used. ...
written 9 weeks ago by
Lior Pachter • 460
4
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... There is a tutorial for how to do that here: https://github.com/BUStools/getting_started/blob/master/kallisto_bus_mouse_nuclei_tutorial.ipynb
This is part of a series of tutorials for how to use kallisto | bustools for a variety of single-cell RNA-seq pre-processing tasks:
[https://www.kallistobus. ...
written 9 weeks ago by
Lior Pachter • 460
• updated
9 weeks ago by
RamRS ♦ 24k
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... Cell Ranger is not a "simple solution" in the sense that it requires large amounts of RAM, large amounts of temporary disk, and takes a very long time to process standard datasets. For example, in benchmarks we performed recently (https://www.biorxiv.org/content/10.1101/673285v2) we found that on th ...
written 12 weeks ago by
Lior Pachter • 460
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... You should not process the FASTQs together, because cell barcodes will clash. So you should process them separately. I would not recommend merging the replicates after processing, information about variance within condition will be useful and important for downstream analysis. If you do aggregate th ...
written 3 months ago by
Lior Pachter • 460
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827
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... RSEM is a widely used tool that produces good results by various benchmarks. On the other hand, a comparison between kallisto and Salmon is pointless because they have been shown in multiple comparisons to produce near identical results. For a recent reference for both these points see https://www.b ...
written 3 months ago by
Lior Pachter • 460
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... Scripts for performing the gene-level differential analysis from the paper you cited are here: https://github.com/pachterlab/aggregationDE
You should be fine with the annotated reference transcriptome as there is no need for a genome for this to work. ...
written 4 months ago by
Lior Pachter • 460
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... It sounds like your goal is to build an index from both the human and the Cassava Brown Steak Virus at the same time. You can do this by obtaining the transcriptomes for each separately, and then building an index using both files:
`kallisto index -i name.idx human.fa.gz cassava_brown_steak_virus.f ...
written 4 months ago by
Lior Pachter • 460
Latest awards to Lior Pachter
Appreciated
6 weeks ago,
created a post with more than 5 votes.
For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Scholar
3 months ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Pundit
3.3 years ago,
created a comment with more than 10 votes.
For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
Appreciated
4.0 years ago,
created a post with more than 5 votes.
For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
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4.2 years ago,
created a comment with at least 3 up-votes.
For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
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