11 Juno-deinterleave
CURRENTLY NOT MAINTAINED OR SUPPORTED
# Parameters
<- list("pipeline_name" = "Deinterleave") parameters
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
- Open a terminal. (Applications>terminal).
- Enter the folder of the pipeline:
cd /mnt/scratch_dir/<my_folder>/deinterleave
- 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