pegi3s/gmap-gsnap 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)

This image facilitates the usage of GMAP-GSNAP⁠, a Genomic Mapping and Alignment Program for mRNA and EST Sequences (GMAP), and a Genomic Short-read Nucleotide Alignment Program (GSNAP).

⁠Using the GMAP-GSNAP image in Linux

You should adapt and run the following command: docker run --rm -v "/your/data/dir:/data" pegi3s/gmap-gsnap bash -c "gmap_build -d <genome_name> -k <k_mer_value> /data/<genome_FASTA_format> && gmap -d <genome_name> /data/input_mRNA > /data/output"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the files you want to analyze.
• <genome_name> to a given name.
• <k_mer_value> to the value of the k-mer size you want to use.
• <genome_FASTA_format> to the genome in FASTA format you want to use.
• input_mRNA to the actual name of your input mRNA FASTA file.
• output to the actual name of your output file.

For instance, if you want to perform a genomic mapping of a Prunus SRNase CDS in a genome file named Prunus.fas, using a k-mer size of 12, you should run: docker run --rm -v "/your/data/dir:/data" pegi3s/gmap-gsnap bash -c "gmap_build -d Prunus -k 12 /data/SRNase_CDS.fas && gmap -d Prunus /data/Prunus.fas > /data/output"

To see the gmap help, just run docker run --rm pegi3s/gmap-gsnap gmap --help.

To see the gmap_build help, just run docker run --rm pegi3s/gmap-gsnap gmap_build --help.

⁠Using the GMAP-GSNAP 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/gmap-gsnap bash -c "gmap_build -d <genome_name> -k <k_mer_value> /data/<genome_FASTA_format> && gmap -d <genome_name> /data/input_mRNA > /data/output"