Deinterleave script

Start the analysis. Basics

Once you have the pipeline downloaded and placed in the right partition, you can start the analysis.

1. Open the terminal.
2. Enter the folder of the pipeline

cd /path/to/<my_folder>/deinterleave

3. Run the deinterleave script

bash deinterleave.sh -i /path/to/<my_folder>/<my_interleaved_file>.fastq.gz

Output

Your two deinterleaved files will be located in the current directory (you can check your current directory by running the command pwd) and they will have the same name than the original file, but with the suffix "_R1" for the forward reads and "_R2" for the reverse reads. For example:

• Original file: sampleX.fastq
• Deinterleaved files:
  • Forward: sampleX_R1.fastq
  • Reverse: sampleX_R2.fastq

Advanced use

Different output folder

There are other commands that might be handy to use. For instance, if you want that the result is saved in a different folder you can do this:

bash deinterleave.sh -i /path/to/<my_folder>/<my_interleaved_file>.fastq.gz -o /path/to/my_results

If the "my results" folder does not exist, it will be created and your resulting deinterleaved files will be stored there.

Choose name of deinterleaved files

You can also use the names you want for the output files. For that you can do:

bash deinterleave.sh -i /path/to/<my_folder>/<my_interleaved_file>.fastq.gz --output_r1 my_deinterleaved_file_R1.fastq --output_r2 my_deinterleaved_file_R2.fastq

Note that I did not use paths there. Your output directory should be set with the option -o

Compress output

You may want to have the deinterleaved files compressed. Note that the compression might take a bit long. For that you can do:

bash deinterleave.sh -i /path/to/<my_folder>/<my_interleaved_file>.fastq.gz --compress

That will make sure that your two interleaved files are gzipped (and have the extension .fastq.gz).

Combine options

It is possible to combine more than one of this options. For example:

bash deinterleave.sh -i /path/to/<my_folder>/<my_interleaved_file>.fastq.gz -o /path/to/my_results --compress