User: Lior Pachter
Lior Pachter • 300
- Reputation:
- 300
- Status:
- Trusted
- Location:
- United States
- Website:
- https://pachterlab.git...
- Twitter:
- @lpachter
- Last seen:
- 6 hours ago
- Joined:
- 3 years, 11 months ago
- Email:
- l*******@caltech.edu
Posts by Lior Pachter
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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 2 days ago by
Lior Pachter • 300
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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 5 days ago by
Lior Pachter • 300
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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 7 days ago by
Lior Pachter • 300
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... There is a blogpost describing how to do this for single-cell RNA-seq here: https://sinabooeshaghi.com/2019/07/09/fasterq-to-count-matrices-for-single-cell-rna-seq/ ...
written 9 days ago by
Lior Pachter • 300
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... See https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth for a useful Snakemake workflow. ...
written 11 days ago by
Lior Pachter • 300
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... The [kallisto | bustools workflow][1] will allow you to specify the barcode / UMI /cDNA read structure and should be helpful for your analysis.
[1]: https://www.kallistobus.tools/ ...
written 24 days ago by
Lior Pachter • 300
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Answer:
A: UMI Tools Dedup
... The [kallisto | bustools workflow][1] has a very low memory footprint.
[1]: https://www.kallistobus.tools/ ...
written 24 days ago by
Lior Pachter • 300
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... It's helpful to look at how the authors of Salmon run Salmon. Sometimes they use
`--seqBias --gcBias --posBias --validateMappings` (see [here](https://github.com/csoneson/annotation_problem_txabundance/blob/master/makefiles/Salmon.mk))
and sometimes they use only `--gcBias` (see [here](https://gith ...
written 25 days ago by
Lior Pachter • 300
• updated
24 days ago by
RamRS ♦ 22k
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... You are right that salmon is similar to kallisto, however kallisto is faster, a relevant matter if one is working on a Mac desktop. https://liorpachter.wordpress.com/2017/08/02/how-not-to-perform-a-differential-expression-analysis-or-science/ ...
written 4 months ago by
Lior Pachter • 300
0
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412
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... You can see an example of a snakemake script to do this with kallisto here:
[https://github.com/pachterlab/bears_analyses]
Not streaming but could be modified to do so. ...
written 10 months ago by
Lior Pachter • 300
Latest awards to Lior Pachter
Pundit
3.0 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
3.7 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
3.9 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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