Moderator: Rob
Rob ♦ 4.5k
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Posts by Rob
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10
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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 8 days ago by
Rob ♦ 4.5k
11
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6
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1.1k
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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 8 days ago by
Rob ♦ 4.5k
2
votes
3
answers
89
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3
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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
Rob ♦ 4.5k
1
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3
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89
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3
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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
Rob ♦ 4.5k
0
votes
1
answer
319
views
1
answers
Comment:
C: How does salmon deal with decoy?
... This is specific to salmon. ...
written 4 weeks ago by
Rob ♦ 4.5k
2
votes
1
answer
319
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1
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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
Rob ♦ 4.5k
1
vote
1
answer
157
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1
answers
... 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
Rob ♦ 4.5k
0
votes
0
answers
194
views
0
answers
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
Rob ♦ 4.5k
0
votes
0
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194
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0
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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
Rob ♦ 4.5k
1
vote
1
answer
167
views
1
answers
... 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
Rob ♦ 4.5k
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For Comparing assembled transcripts against a reference
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