Moderator: Rob
Rob ♦ 4.6k
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- @nomad421
- Last seen:
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- 10 years ago
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Posts by Rob
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2
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... STARsolo is *not* STARsolo-Quant. STARsolo is the single-cell mode of STAR that is actively developed, maintained, and improved. It is usable today as a (much more efficient) and near drop-in replacement of Cell Ranger. It uses a UMI resolution algorithm specifically designed to be very similar t ...
written 12 days ago by
Rob ♦ 4.6k
1
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... As far as I am aware, neither Cell Ranger, nor STARSolo "handle" gene ambiguous reads. Such reads are discarded by those pipelines, as the UMI resolution algorithm assumes related UMIs --- UMIs that will be deduplicated --- align to the same gene. ...
written 13 days ago by
Rob ♦ 4.6k
2
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1
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182
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1
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... I would be tempted to post this (with the generating data and some specific pointers to these cases) to the [STAR](https://github.com/alexdobin/STAR) repository. Alex Dobin is very responsive, and at the very least, can likely give you a definitive answer as to why you're seeing this behavior. ...
written 5 weeks ago by
Rob ♦ 4.6k
3
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... Salmon is quite easy to use. You can check out the getting started documentation here (https://combine-lab.github.io/salmon/getting_started/) and the full documwntation here (https://salmon.readthedocs.io/en/latest/). If you have any questions where you don't find answers here or in the FAQ, feel ...
written 7 weeks ago by
Rob ♦ 4.6k
10
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6
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1.6k
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6
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... Part (2/2):
Finally, I would be remiss if I didn't mention that there clearly _are_ some benefits to (modern) C++. First, if you choose C++, I would set a minimum version no earlier than C++17. It adds a lot of important and nice new features that make writing clean, expressive and efficient code ...
written 3 months ago by
Rob ♦ 4.6k
11
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6
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1.6k
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6
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... The forum only supports answers up to 5k characters, so this answer is broken into 2 parts (1/2):
This is an interesting question, and I think the answer depends on what your primary goal is. Istvan makes good points in favor of straight-forward C (integrated with Python) for building tools that a ...
written 3 months ago by
Rob ♦ 4.6k
2
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3
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307
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3
answers
Comment:
C: update salmon with conda
... Let me tag @Devon Ryan here as well, since he may have an idea what's going on with bioconda. ...
written 3 months ago by
Rob ♦ 4.6k
1
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3
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307
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3
answers
Answer:
A: update salmon with conda
... Have you tried `conda install salmon=1.3.0`, to specifically request the latest version? Sometimes, there are strange package conflicts, and so the other thing you can try is to create a new, blank, environment, and install salmon there. ...
written 3 months ago by
Rob ♦ 4.6k
0
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1
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755
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1
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Comment:
C: How does salmon deal with decoy?
... This is specific to salmon. ...
written 3 months ago by
Rob ♦ 4.6k
3
votes
1
answer
755
views
1
answers
Comment:
C: How does salmon deal with decoy?
... Hi Assa,
Sure. The decoy sequences are regions of the target *genome* that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping (e.g. transcribed pseudogenes, etc.). There are 3 ways to run salmon : (a) with *just* the annotated tra ...
written 3 months ago by
Rob ♦ 4.6k
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For A: Error in Transcript to gene level estimation using "Genesum" package
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For A: Error in Transcript to gene level estimation using "Genesum" package
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For A: Error in Transcript to gene level estimation using "Genesum" package
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