User: lakigigar
lakigigar • 210
- Reputation:
- 210
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- United States
- Website:
- http://math.berkeley.e...
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- @lpachter
- Last seen:
- 4 months, 2 weeks ago
- Joined:
- 3 years, 5 months ago
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Posts by lakigigar
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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 4 months ago by
lakigigar • 210
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... There are a few conceptual issues that might help you in the analysis:
1. You said you aligned the reads with STAR to the UMD3.1 cattle genome. With such alignments you cannot quantify using salmon. To use Salmon you'll need to work with a transcriptome, available from here ftp://ftp.ensembl.org/pu ...
written 16 months ago by
lakigigar • 210
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... I strongly recommend you replace your tophat+cufflinks+cuffdiff2 pipeline with kallisto+sleuth. ...
written 2.5 years ago by
lakigigar • 210
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... https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ ...
written 2.8 years ago by
lakigigar • 210
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Comment:
C: RNA-Seq for DE analysis
... Using sleuth it is straightforward to examine quantification at the gene level. In a forthcoming release imminent there will be ability to perform differential analysis directly at the gene level as well as well. ...
written 2.8 years ago by
lakigigar • 210
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Comment:
C: RNA-Seq for DE analysis
... As an author of Cufflinks I strongly recommend that you switch to kallisto http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3519.html and sleuth for differential analysis. You can start here http://pachterlab.github.io/sleuth/ with an introduction and example here https://rawgit.com/pachterl ...
written 2.8 years ago by
lakigigar • 210
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... You might find http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3519.html to be useful. It is focused precisely on the issue of how to accurately assign multi-mapping reads for RNA-Seq abundance estimation. ...
written 2.8 years ago by
lakigigar • 210
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... Sleuth performs best when used with bootstraps from kallisto. We find significant performance improvements when doing that as opposed to feeding estimated transcript counts into tools such as DESeq2 or edgeR. ...
written 2.8 years ago by
lakigigar • 210
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... For differential analysis it is strongly recommended to use Sleuth; see this thread https://www.biostars.org/p/157240/ ...
written 2.8 years ago by
lakigigar • 210
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... It is true that Sailfish was updated after the kallisto paper was submitted. The current version (0.9.2) incorporates many of the key elements of kallisto (pseudoalignment, the kallisto bias correction and the kallisto effective length correction) so that it is now practically identical to kallisto ...
written 2.8 years ago by
lakigigar • 210
Latest awards to lakigigar
Pundit
2.5 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
3.2 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
3.4 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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