pegi3s/cutadapt repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

⁠Using the Cutadapt image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/cutadapt -u 10 /data/input.fq -o /data/output.fq

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file you want to process.
• input.fq to the actual name of your input file.
• output.fq to the actual name of your output file.

A negative value after -u would trims reads at the end.

To see the Cutadapt⁠ help, just run docker run --rm pegi3s/cutadapt -h.

⁠Test data

To test the previous command, you can download this FASTQ compressed file⁠ (1.1GB). Note that it does not need to be decompressed as Cutadapt can deal with both compressed and uncompressed fastq files.

In the previous command you just need to replace /data/input.fq with /data/sra_data.fastq.gz. You can also speed up the execution by adding -j 4 to tell Cutadapt to use 4 cores (it uses 1 core by default).

Note: processing this file ends up with the following error because of an extra line at the end of the FASTQ, but the output file contains the correct result.

cutadapt.seqio.FormatError: Line 1 in FASTQ file is expected to start with '@', but found '\n'
cutadapt: error: Line 1 in FASTQ file is expected to start with '@', but found '\n'

⁠Using the Cutadapt image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/cutadapt -u 10 /data/input.fq -o /data/output.fq