You can read about salmon’s many options in the documentation.Īfter the salmon commands finish running, you should have a directory named quants, which will have a sub-directory for each sample. However, the purpose and behavior of all of those options is beyond the scope of this introductory tutorial. Salmon exposes many different options to the user that enable extra features or modify default behavior. Finally, the -p 8 argument tells salmon to make use of 8 threads and the -o argument specifies the directory where salmon’s quantification results sould be written. The -1 and -2 arguments tell salmon where to find the left and right reads for this sample (notice, salmon will accept gzipped FASTQ files directly). The -i argument tells salmon where to find the index -l A tells salmon that it should automatically determine the library type of the sequencing reads (e.g. This script simply loops through each sample and invokes salmon using fairly barebone options.
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