11 Juno-deinterleave

CURRENTLY NOT MAINTAINED OR SUPPORTED

# Parameters
parameters <- list("pipeline_name" = "Deinterleave")

11.1 Handbook

11.1.1 Requirements and preparation

See the General Instructions for all pipelines first.

11.1.2 Download the pipeline

YOU NEED TO DOWNLOAD THE PIPELINE ONCE OR EVERY TIME YOU WANT TO UPDATE IT

Please follow the instructions to download pipelines from the Juno team of the IDS-bioinformatics group. The Myco-lofreq pipeline can be found in this link.

11.1.3 Start the analysis. Basics

  1. Open a terminal. (Applications>terminal).
  2. Enter the folder of the pipeline:

cd /mnt/scratch_dir/<my_folder>/deinterleave
  1. Run the deinterleave script

bash deinterleave.sh -i /mnt/scratch_dir/<my_folder>/<my_interleaved_file>.fastq.gz

11.1.4 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

Note: If you want your output to be stored in a folder with a different name or location, you can use the option -o (from output)


bash deinterleave.sh -i /mnt/scratch_dir/<my_folder>/<my_interleaved_file>.fastq.gz -o /mnt/scratch_dir/my_results

11.1.5 Extra options

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 /mnt/scratch_dir/<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 /mnt/scratch_dir/<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 /mnt/scratch_dir/<my_folder>/<my_interleaved_file>.fastq.gz -o /mnt/scratch_dir/my_results --compress