How do I fill in the Sample File for my QuantSeq data analysis?
The Sample File (sample_file.csv) for QuantSeq data analysis can be downloaded from this Webpage.
Please do not change the name of the Sample File. The name of the Sample File must be sample_file.csv.
The Sample File is a .csv file that includes four columns separated by commas. The names of the columns are:
1- Sample_Name
2- File_Name_R1
3- Condition_ID (Optional)
4- File_Name_R2 (Optional)
The Condition ID needs to be specified only if differential gene expression analysis (DE) is required. The File_Name_R2 column is only required for PE sequencing, when Read 2 files are also uploaded.
ATTENTION! If Condition ID and File_Name_R2 are not required, these fields need to be left EMPTY.
Examples:
Sample File filled in for SR data (Read 1 only) with no DE analysis required
Sample File filled in for PE data (Read 1 and Read 2 are provided) including DE analysis
In the .csv file, each row represents the information related to a single FASTQ file.
What does each column refer to?
1- The column “Sample_Name” refers to the name of the specific sample. The sample name can be any combination of letters, numbers, the dot “.” and the underscore “_” signs. The same sample name must be repeated for all the FASTQ files that have to be merged (see also “How do I specify to merge my files in my Sample Definition File?”).
Example:
ATTENTION! Please, for the sample name use only the characters listed above (letters, numbers, the dot and the underscore signs). Do not use any other additional characters/symbols (including the space “ “) when specifying a name.
Example:
Correct: ”S_Cerevisiae_CTRL”
Incorrect: “S_Cerevisiae CTRL”
2- The columns File_Name_R1 (mandatory) and File_Name_R2 (optional) refer to the exact name of the FASTQ files to analyze. The FASTQ files must be compressed with gzip. The name of the FASTQ files should include the correct file extension and the directory name, if necessary. For the file name, the dot symbol “.” is required to specify the file extension (e.g., file_name.fastq.gz). If FASTQ files are uploaded into a subdirectory of the directory “upload” (generated in the user’s sFTP account), only the subdirectories of the “upload” directory should be included in the FASTQ file name.
Example of file name:
Correct: ”/Subdirectory_name/File_Name_R1_001.fastq.gz”
Incorrect: ”/Subdirectory_name/File_Name_R1_001”
3- The column Condition_ID refers to the name of the experimental condition of your sample. This name can be any combination of letters, numbers, the dot “.” and the underscore “_" signs. An experimental condition can be shared by several samples.
Example:
Sample1, Sample2, and Sample3 are replicates of the same condition (e.g., Control samples). Therefore, they should all be labeled with the same Condition_ID (e.g., CTRL”, or “C1”, or any other name that can be easily identified).
ATTENTION! Please, for the Condition_ID name use only the characters listed above (letters, numbers, the dot and the underscore signs). Do not use additional characters/symbols (including the space “ “) when specifying a name for the sample condition.
ATTENTION! The Condition_ID must be filled in when differential gene expression analysis is required (DeSeq2). If there is no need for differential gene expression analysis, the column should be left empty.
Please, keep the sample name and the condition ID short, when possible.