User: Lior Pachter

gravatar for Lior Pachter
Lior Pachter530
Reputation:
530
Status:
Trusted
Location:
United States
Website:
https://pachterlab.git...
Twitter:
@lpachter
Last seen:
5 months, 2 weeks ago
Joined:
5 years, 1 month ago
Email:
l*******@caltech.edu

Posts by Lior Pachter

<prev • 40 results • page 1 of 4 • next >
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Comment: C: How to get read counts on transcript level using featurecounts?
... 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 7 months ago by Lior Pachter530
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Comment: C: How to get read counts on transcript level using featurecounts?
... 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 7 months ago by Lior Pachter530
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Comment: C: How to get read counts on transcript level using featurecounts?
... Yes you can. See http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html ...
written 7 months ago by Lior Pachter530
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Comment: C: How to get read counts on transcript level using featurecounts?
... 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 7 months ago by Lior Pachter530
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Comment: C: Kallisto in snakePipes instead of salmon
... 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 7 months ago by Lior Pachter530 • updated 7 months ago by RamRS30k
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Comment: C: Cellranger data to Monocle Pseudotime
... 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 7 months ago by Lior Pachter530
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Comment: C: Should I merge the Paired-end RNA-seq reads for BLAT for intron identification
... 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 8 months ago by Lior Pachter530
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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 10 months ago by Lior Pachter530
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Answer: A: RNA-Seq quantification of a heterozygous individual with a short deletion
... You should modify your transcriptome to include both haplotypes for the gene. ...
written 11 months ago by Lior Pachter530
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Answer: A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
... 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 12 months ago by Lior Pachter530

Latest awards to Lior Pachter

Scholar 12 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Scholar 12 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Scholar 14 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Pundit 4.2 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.
Commentator 5.0 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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