Moderator: Rob
Rob ♦ 2.8k
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... Is the data paired-end? In this case, salmon estimated the fragment length distribution. In the quantification directory the file `libParams/flenDist.txt` contains the parameters of the normalized distribution of observed fragment lengths. Each of the 1001 numbers gives the probability of observi ...
written 26 days ago by
Rob ♦ 2.8k
1
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1
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235
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... You can reduce the memory required by star by building the index with the `--genomeSAsparseD` parameter set to a value greater than 1. This samples the suffix array. If the value is too large, STAR will become slower, but small values (e.g. 2/4) can provide a nice memory savings without slowing th ...
written 28 days ago by
Rob ♦ 2.8k
1
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1
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... No. STAR has the ability to perform a single alignment against genome (and gtf), and to provide 2 separate outputs using the same alignments. One BAM file contains the spliced alignments to the genome. The other BAM file contains the unspliced alignments to the transcriptome (suitable to provide ...
written 28 days ago by
Rob ♦ 2.8k
1
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1
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235
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1
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... In this case, as I suggested, the easiest path is to align with STAR and keep both the genome alignments and get the transcriptome alignments. As swbarnes2 mentions below, you can even use STARs `--quantMode` for the genome-level counts. Note, however, that you won't be able to get transcript leve ...
written 29 days ago by
Rob ♦ 2.8k
0
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1
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1
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... I see. In that case, perhaps consider aligning with STAR, which can give you both the genome and transcriptome alignments at the same time. The genome alignments can be counted using featureCounts, and the transcriptome alignments can be fed to salmon for transcript-level quantification. Also, it ...
written 29 days ago by
Rob ♦ 2.8k
0
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1
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235
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1
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... Did you align against the genome or transcriptome? If you want to use a traditional aligner to provide input to salmon (rather than using its builtin mapping algorithm), then you should either (1) align to the genome with STAR and tell it to project the alignments to the transcriptome (it can do th ...
written 4 weeks ago by
Rob ♦ 2.8k
1
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339
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... The effect of the `--geneMap` flag is to cause salmon to output, in addition to it's transcript level quantifications, aggregated gene-level quantifications. However, this flag exists only for backward compatibility and is deprecated in favor of tximport. Though it attempts to do the same thing, t ...
written 4 weeks ago by
Rob ♦ 2.8k
1
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2
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339
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2
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... I'd recommend going with the quasi-mapping, and including the `--validateMappings` option among your command line flags (including others that seem relevant for your data given the documentation). ...
written 5 weeks ago by
Rob ♦ 2.8k
1
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339
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2
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... As you point out, whether or not you use traditional alignment pr the builtin mapping algorithm, you won't be finding novel isoforms. If you want to do that, you should perform assembly via a tool like Stringtie or Scallop prior to quantification.
Regardless of if you do that, if you want to use ...
written 5 weeks ago by
Rob ♦ 2.8k
1
vote
2
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339
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2
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... Wait; did you align against the transcriptome using TopHat2? I would highly recommend against doing that. In alignment-based mode, salmon requires alignments to the transcriptome. The best ways to obtain such alignments are either to (1) align to the genome using STAR and use it's built-in facilit ...
written 5 weeks ago by
Rob ♦ 2.8k
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