parameters mapping in salmon software
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19 months ago

Hello, I am writing a paper and they ask me for the mapping parameters of the salmon software, do I need to know what these default parameters are for the quasi- mapping in the salmon? Regards!!

alignment RNA-Seq • 504 views
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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 to expect you to know all of the default values that a particular tool sets (this is why providing the version of the tool is also important).

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I understand what you are telling me but the magazine requests to complete an excel file with the details of the rna seq. I did not do this analysis myself, but I imagine that the mapper should have default parameters. I need to know these parameters since I have searched for them and cannot find them. thanks for your answer

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magazine requests to complete an excel file

I assume you mean a scientific publication.

I need to know these parameters since I have searched for them and cannot find them.

@Rob is the author of Salmon software. As he indicated no one should expect you to list all parameters for a software. In fact many may not be listed in the in-line help or manual. You would need to examine the code to find some of this information. As @Rob suggested, listing the version of the software should be fully adequate for any reputable scientific publication. That should allow anyone to reproduce your analysis.

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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 implicit if nothing is provided on the command line. However, the version of the software and the precise command line provides a full description of how the tool was run, and that should be sufficient for any publication.

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