User: Lior Pachter
Lior Pachter • 540
- Reputation:
- 540
- Status:
- Trusted
- Location:
- United States
- Website:
- https://pachterlab.git...
- Twitter:
- @lpachter
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 5 years, 5 months ago
- Email:
- l*******@caltech.edu
Posts by Lior Pachter
<prev
• 40 results •
page 1 of 4 •
next >
0
votes
3
answers
1.7k
views
3
answers
... Your question is answered in detail in the paper (by the way, to be clear, it is not my paper and I had nothing to do with it). ...
written 10 months ago by
Lior Pachter • 540
1
vote
3
answers
1.7k
views
3
answers
... The estimation of transcript-level counts is necessary to obtain accurate gene-level abundance estimates, so it should be done even if only interested in genes and not transcripts *per se*. See, e.g. https://www.youtube.com/watch?v=5NiFibnbE8o ...
written 10 months ago by
Lior Pachter • 540
0
votes
3
answers
1.7k
views
3
answers
... Yes you can. See http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html ...
written 10 months ago by
Lior Pachter • 540
0
votes
3
answers
1.7k
views
3
answers
... The paper linked to concludes that:
"Because both Kallisto and Salmon performed highly concordantly with the ground truth, they were also highly concordant with each other, as previously reported [34,35]. They cluster together in the method similarity matrix before clustering with the ground truth ...
written 10 months ago by
Lior Pachter • 540
1
vote
1
answer
456
views
1
answers
... Wow. [Your paper on snakePipes](https://academic.oup.com/bioinformatics/article/35/22/4757/5499080) states "snakePipes provides a set of best-practices workflows". Yet it seems you're not interested at all in providing users best-practice workflows, rather you're using your tool to exercise a person ...
written 11 months ago by
Lior Pachter • 540
• updated
11 months ago by
_r_am ♦ 32k
1
vote
1
answer
1.0k
views
1
answers
... Here is a tutorial for how to convert 10x data to Monocle pseudotime: https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/notebooks/kb_monocle.ipynb
The tutorial goes from reads to results, and is on Google Colab so you can run it in a browser. ...
written 11 months ago by
Lior Pachter • 540
1
vote
1
answer
390
views
1
answers
... RNA-seq reads do not contain the non-canonical splice site sequences that are located in introns. That issue is therefore moot if you are using option B with a transcriptome from your genome. ...
written 12 months ago by
Lior Pachter • 540
2
votes
1
answer
1.8k
views
1
answers
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 14 months ago by
Lior Pachter • 540
2
votes
1
answer
286
views
1
answers
... You should modify your transcriptome to include both haplotypes for the gene. ...
written 15 months ago by
Lior Pachter • 540
5
votes
3
answers
7.1k
views
3
answers
... 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 15 months ago by
Lior Pachter • 540
Latest awards to Lior Pachter
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Single-nucleus RNA-seq processing (10x) with Pseudoaligners (Kallisto)
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
Appreciated
15 months 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
15 months ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Scholar
16 months ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Scholar
17 months ago,
created an answer that has been accepted.
For A: about the use of CellRanger aggr
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: about the use of CellRanger aggr
Pundit
4.5 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
5.2 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.
Commentator
5.3 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.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1826 users visited in the last hour