Moderator: Rob
Rob ♦ 4.0k
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Posts by Rob
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2
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1
answer
90
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... Hi @ruiyan_hou,
Alevin does not perform transcript-level quantification from tagged-end single-cell RNA-seq data. As far as I am aware, there is no tool that outputs transcript-level abundances (i.e. a transcript x cell matrix) from such data. This is because tagged-end single-cell data — at le ...
written 8 days ago by
Rob ♦ 4.0k
0
votes
1
answer
126
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1
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... Right, you need the bam in transcriptomic coordinates. If you have that, you can already run salmon on it. ...
written 12 days ago by
Rob ♦ 4.0k
2
votes
1
answer
85
views
1
answers
Answer:
A: Trimmomatic and Salmon error
... It looks like you have an inconsistent set of modules loaded on the nodes where younare running? Can you run the software successfully from the submit node? If so, then you need to replicate the loased modules and paths in your job script. It's usually a bit more pain to get thimgs working acros ...
written 26 days ago by
Rob ♦ 4.0k
1
vote
0
answers
178
views
0
answers
... In your command, you have a space between `--` and `type`. There shoild be no space there. Also, for recent versions of salmon (1.0.0 and later), there is no `quasi` index type. The new index type is called `puff`, but you can leave off the `--type` argument all together and just try:
```
salmon ...
written 4 weeks ago by
Rob ♦ 4.0k
0
votes
0
answers
178
views
0
answers
... It sounds like the salmon executable is not in your path. What do you get if you simply write:
`which salmon`
at your command prompt? How did you install salmon? ...
written 4 weeks ago by
Rob ♦ 4.0k
1
vote
0
answers
164
views
0
answers
... Yes, you can use salmon when you have long reads — however, you should use alignments generated with a long-read oriented aligner rather than salmon's inbuilt selective-alignment (which has not been thoroughly tested with long reads yet). There is a pipeline for long read quantification that makes ...
written 6 weeks ago by
Rob ♦ 4.0k
3
votes
1
answer
213
views
1
answers
... Since this is full length without UMIs, salmon would be the tool to use here. Out of curiosity, how did you obtain the pile-up? How do you know those are all reads coming from this transcript? Is it a single transcript gene? You can always align the reads with STAR and get a bam file using `—qua ...
written 6 weeks ago by
Rob ♦ 4.0k
0
votes
2
answers
371
views
2
answers
... That is still quite low, of course. By "projected to the transcriptome", I mean using STAR's `--quantMode TranscriptomeSAM`, and getting rid of the sorting by coordinate (basically, the parameters that RSEM uses with STAR as the aligner, except also allowing indels in the alignment). This will at ...
written 10 weeks ago by
Rob ♦ 4.0k
1
vote
2
answers
371
views
2
answers
... What is the correlation among expression estimates? If there is little to no true DE, then logFCs will be close to 0 for many genes and correlations will be quite low. Have you tried quantifying with salmon using STAR's mappings (projected to the transcriptome)? ...
written 10 weeks ago by
Rob ♦ 4.0k
2
votes
1
answer
158
views
1
answers
... It is O(mnk), and for each new sequence, there is a multiplicative factor of the new sequence's length. This is why MSA is intractable in the general case to solve optimally. See e.g. https://www.cs.cmu.edu/~ckingsf/bioinfo-lectures/msa.pdf. ...
written 10 weeks ago by
Rob ♦ 4.0k
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For A: Error in Transcript to gene level estimation using "Genesum" package
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