In this example, sample names appear in column 30, and we can parse the information we need with the following: cat runinfo.csv | cut -f 1 -d, | grep SRR > runids.txtĬat runinfo.csv | cut -f 1,30 -d, > run_sample_name.csvĬat run_sample_name.csv | sed 's/,/\t/' | grep SRR > run_sample_names.tsv This is a frustration because without it, it is likely not possible to replicate a published result. All meta data should be included but it is not required to be complete. Search the other columns for sample names or something else that can be used to construct meaningful sample names. ![]() These ID’s are unique but otherwise meaningless. The first column contains the ID’s for the run (i.e. ![]() Download run information from the project PRJNA524467, or another project of your choosing, to the file runinfo.csv with the following command from your own project directory: esearch -db sra -query PRJNA524467 | efetch -format runinfo > runinfo.csvĮxamine the file by opening it in a spreadsheet program. The first step is to fetch information about the project.
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