Moderator: Rob

gravatar for Rob
Rob4.5k
Reputation:
4,450
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Location:
United States
Twitter:
@nomad421
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an hour ago
Joined:
9 years, 9 months ago
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r********@gmail.com

Posts by Rob

<prev • 263 results • page 1 of 27 • next >
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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 8 days ago by Rob4.5k
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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 8 days ago by Rob4.5k
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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 8 days ago by Rob4.5k
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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 8 days ago by Rob4.5k
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Comment: C: How does salmon deal with decoy?
... This is specific to salmon. ...
written 4 weeks ago by Rob4.5k
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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 4 weeks ago by Rob4.5k
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Answer: A: Gibbs sampling/bootstrap replicates in Salmon
... Hi @Dunois, Thanks for the follow-up. You’re absolutely right that there’s not a lot of documentation around for using the posterior estimates _for this purpose_. Currently, the most common uses of these estimates are to improve transcript-level differential expression, as outlined here (http://w ...
written 4 weeks ago by Rob4.5k
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Comment: C: Transcripts with no read support
... Hi @Dunois, Regarding the selective-alignment paper, that is a general improvement to the mapping methodology, so the main application of that paper to this context is just to make sure you're using the most recent version of salmon that implements these improvements (which it seems you are doing ...
written 6 weeks ago by Rob4.5k
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Comment: C: Transcripts with no read support
... In addition to Lieven’s excellent comments, I wanted to ask an orthogonal question about the process here. Has the assembly been performed from a collection of different samples? And if so, is this 0 read support transcript discovered in each individual sample, or across all samples, or across the ...
written 6 weeks ago by Rob4.5k
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Answer: A: How can I align single RNA seq(scRNAseq) data by using STAR or another aligner?
... STAR has a "STARSolo" mode specifically for dealing with tagged-end single cell data. Check the STAR manual and search for "STARSolo". The tool is well-documented. ...
written 6 weeks ago by Rob4.5k

Latest awards to Rob

Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Convert a FASTA Amino Acid Sequence to RNA (Reverse Central Dogma)
Good Answer 8 days 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....
Appreciated 8 days 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 8 days ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Getting sequence id from k-mers using jellyfish
Good Answer 10 days 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 weeks ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
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?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Teacher 12 weeks 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
Scholar 5 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Scholar 6 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Teacher 6 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 6 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 8 months ago, created an answer that has been accepted. For A: Error in Transcript to gene level estimation using "Genesum" package
Appreciated 10 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?
Good Answer 10 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 11 months ago, created an answer with at least 3 up-votes. For A: How Scores are given in Substitution matrix like PAM and BLOSUM?
Student 12 months ago, asked a question with at least 3 up-votes. For Comparing assembled transcripts against a reference

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