Moderator: Rob

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Rob4.6k
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@nomad421
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Posts by Rob

<prev • 267 results • page 1 of 27 • next >
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Comment: C: How to change cellranger multimapping algorithm
... 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 Rob4.6k
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Comment: C: How to change cellranger multimapping algorithm
... 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 Rob4.6k
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Comment: C: RNA-Seq junction reads overhang imbalance
... 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 Rob4.6k
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Answer: C: Quantify Isoforms in RNA-Seq data
... 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 Rob4.6k
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Answer: A: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... 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 Rob4.6k
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Answer: A: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... 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 Rob4.6k
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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 Rob4.6k
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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 Rob4.6k
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Comment: C: How does salmon deal with decoy?
... This is specific to salmon. ...
written 3 months ago by Rob4.6k
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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 Rob4.6k

Latest awards to Rob

Scholar 15 days ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Convert a FASTA Amino Acid Sequence to RNA (Reverse Central Dogma)
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Getting sequence id from k-mers using jellyfish
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Scholar 4 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Scholar 7 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Scholar 8 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Scholar 9 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: C++ tools are hard to install for biologist, why the community stick on it?
Scholar 10 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Appreciated 13 months ago, created a post with more than 5 votes. For C: C++ tools are hard to install for biologist, why the community stick on it?

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