Batch file name conversion

In many cases, sample names used during sequencing might not be easy for identifying samples during the analysis, particularly if user want to label samples by their group properties (e.g., treatment, time point, etc.), or biological replicates. Here, we provide a utility script to replace the sample names in the file names with user-defined label.

Given a comma-separated (csv) file containing sample names (used in the files) and a user-refined label, the script will replace the sample names in the file names while remaining the file extension for all files in a given directory.

It is important to note that the script must contain two columns:

• Sample: the original sample name, should match the sample names in the file names
• Label: the user-defined label to replace the sample name

Using this csv file, users can regard it has a sample tracking sheet, and can contain additional metadata information for each sample. For example, in ChIP-seq experiments, the csv file can contain the following columns:

• Sample: the original sample name
• Label: the user-defined label
• Group: the grouping condition
• Batch: the batch number
• Replicate: the biological replicate number
• Mark: the antibody used

This is performed using the file_name_conversion.py script, which can be found here.

To use the script, users can run the following command:

python3 file_name_conversion.py <path_to_csv_file> <path_to_directory> <file_extension>

For example: s1_H3K27_bowtie2.bam could be a bad file naming for analysis. Given a csv file containing the following information:

Sample	Label	Treatment	Batch	Replicate	Mark
s1_H3K27	ctrl1_H3K27me3_rep1	Control	1	1	H3K27me3

Running the script with the following command:

python3 file_name_conversion.py sample_tracking.csv /path/to/directory/ _bowtie2.bam

will rename the file to ctrl1_H3K27me3_rep1_bowtie2.bam.

To generate a basic sample matrix csv file, users can use the generate_sample_matrix.py script as described here.