Moderator: Rob
Rob ♦ 2.0k
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3
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143
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... HISAT2 can probably be cajoled into aligning to the transcriptome directly, but it is designed to perform spliced read alignment to the genome directly. Bowtie2, on the other hand, is designed to map reads continuously to the indexed reference. It just happens to be particularly good at dealing wi ...
written 7 days ago by
Rob ♦ 2.0k
3
votes
1
answer
138
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1
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... Just for future reference, this can also be done with salmon using the [--writeMappings](http://salmon.readthedocs.io/en/latest/salmon.html#writemappings) flag. However, it's probably worth noting that the pseudo-SAM files produced by these programs are mapping records of fragments directly to the ...
written 10 days ago by
Rob ♦ 2.0k
1
vote
1
answer
143
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1
answers
Answer:
A: Reference for Salmon
... Yes, if you prepare a reference with rsem-prepare-reference it will work with salmon. ...
written 20 days ago by
Rob ♦ 2.0k
4
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1
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103
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1
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... Hi Charles,
The issue is that the libtype flag `-l` (short form) or `--libType` (long form) requires an argument. In your case, this would be `U` for unstranded. So, your full command would look like:
`cm@node10:~/mouseRNAseq$ salmon quant -i mouseRNA_index -l U -r ./fastq/S1_R1.fastq.gz -p 8 ...
written 21 days ago by
Rob ♦ 2.0k
1
vote
1
answer
192
views
1
answers
Comment:
C: tophat 2 rna seq
... Hi dimitrischat,
It's worth noting that TopHat2 has been, essentially, [deprecated by the developers](https://ccb.jhu.edu/software/tophat/index.shtml), who recommend using HISAT2 instead. Unless you have a very specific reason to adopt TopHat2 in your pipeline, it's probably best to follow their ...
written 27 days ago by
Rob ♦ 2.0k
2
votes
1
answer
144
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1
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... Hi biks.kestro,
I just had a chance to respond to this on the salmon/sailfish user group [here](https://groups.google.com/d/msg/Sailfish-users/m1_vlC_jcu8/uJwBYPYIAwAJ). Please note that I moved your original post there since it was submitted as a response to our survey announcement rather than ...
written 28 days ago by
Rob ♦ 2.0k
2
votes
1
answer
140
views
1
answers
... The issue is that you have samples where no reads are mapping. When there are no reads, there is no meaningful relative abundance of transcripts. I've recently (in the develop branch of salmon) changed the default behavior to be to warn the user and output a `quant.sf` file with all 0 TPMs. Howev ...
written 6 weeks ago by
Rob ♦ 2.0k
1
vote
1
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131
views
1
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... By combining the samples prior to assembly, you increase the likelihood of generating (computationally) chimeric transcripts. You might try to assembly separately and then combine the assemblies using e.g. [TACO](https://tacorna.github.io). Also, TopHat has been deprecated by the developers. For ...
written 7 weeks ago by
Rob ♦ 2.0k
1
vote
1
answer
217
views
1
answers
... Methods that implement effective length correction all avoid generating negative effective lengths. Actually, they do this in quite a few different ways (depending on the tool).
Actually, however, it might be most useful to think of the "effective length" as a property of both a transcript and a ...
written 8 weeks ago by
Rob ♦ 2.0k
1
vote
1
answer
282
views
1
answers
Comment:
C: Converting TPM to FPKM
... Why would you do this, rather than converting FPKM to TPM? There is no benefit to FPKM over TPM and the FPKM to TPM conversion is trivial. ...
written 11 weeks ago by
Rob ♦ 2.0k
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