Moderator: Rob
Rob ♦ 3.7k
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Comment:
C: hisat2 salmon alignment error
... No, this will simply prevent HISAT2 from aligning reads outside of annotated transcripts. These will still be spliced alignments in genomic coordinates. As far as I know, HISAT2 has no option to project genomic alignments to transcriptomic coordinates, so the only way to accomplish this with HISAT ...
written 8 days ago by
Rob ♦ 3.7k
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Answer:
A: hisat2 salmon alignment error
... You aligned your reads to the *genome* with HISAT2, and you are trying to quantify the transcriptome with salmon. The references are not the same, and salmon does not (currently) support consuming genome-aligned BAM files for transcriptome quantification. You either need to align the reads directl ...
written 8 days ago by
Rob ♦ 3.7k
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... If you have access to the quantification directories output by salmon, then, within each directory, the `cmd_info.json` file encodes the precise command line parameters passed to salmon that generated the quantification results. Again (and as @genomax denotes above), default parameters are often im ...
written 14 days ago by
Rob ♦ 3.7k
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... I would recommend you state in your manuscript the specific version of the software you used, as well as all relevant parameters you passed via the command line. You should ideally do this for all the software tools you used in your paper. However, it is not typical (or reasonable) for a reviewer ...
written 15 days ago by
Rob ♦ 3.7k
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... By default, the mapping information is not written out. If you run salmon with the `--writeMappings` flag, and give it a file to write the mappings to, then it will write a SAM file with the mappings it generated. ...
written 4 weeks ago by
Rob ♦ 3.7k
3
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... Yes; in general the ability to distinguish between similar transcripts should be quite good. Of course, it depends on the exact read evidence. If the reads deriving from these transcripts overlap very few (or no) variants, then there is no specific evidence of the presence of one transcript versus ...
written 4 weeks ago by
Rob ♦ 3.7k
1
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... The reason salmon gives this message is because the Gencode transcripts have (for the purposes most people want to use them for) unnecessarily long and convoluted names. Specifically, there is the transcript id, and then a considerable amount of metadata encoded in the record name, separated by `|` ...
written 5 weeks ago by
Rob ♦ 3.7k
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... Hi jrleary,
I don't have an answer for this, but I can say that `Run human only on original .fasta` is not an error message generated by salmon itself. Are there some extra checks that happen when you submit your job? ...
written 9 weeks ago by
Rob ♦ 3.7k
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...
Hello harshraje19!
Questions similar to yours can already be found at:
Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why ...
written 3 months ago by
Rob ♦ 3.7k
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... It looks as though the index is being created properly. What is the output of the mapping phase? Have you looked at all at the SAM file being produced? Does that contain records that look like valid mappings? ...
written 3 months ago by
Rob ♦ 3.7k
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