frederic-mahe/neotropical-soils-submission

prepare and format metadata for a EBI/ENA submission of the Neotropical metabarcoding data

Neotropical soils submission

prepare and format metadata for a EBI/ENA submission of the Neotropical metabarcoding data

tasks

• start the project,
• clone,
• create folders,
• add placeholders,
• start a Rmd file,
• check that I have metadata entries for all samples (454 and Illumina),
• fetch per-sample geographical coordinates,
• add a free-form column with a description for each sample,
• replicate the structure of the file neotrop_samples.tsv.csv, the second line of headers is lifted from a eukbank submission template downloaded today (2022-11-24),
• add columns one-by-one,
• reorder columns if need be, create new ones if need be,
• check primer sequences,
• set depth to zero
• issues with samples T185-186 (need to rename fastq files), T199_T200, and L137_L13

get a list of all available read files (SFF and fastq)

# aragorn
cd ${HOME}/projects/neotropical-soils-submission/data/

(
    cd ${HOME}/projects/Ciliata_neotropical/data/
    echo -e "run\tSubmitted_files"
    (
        find . -name "*.sff"
        find ./201*/ -name "*.fastq.*" | \
            grep -vE "_P[13]_|_NT[13]_|_K[14]_|_H?T[13]_"
    ) | \
        sort | \
        tr "/" "\t" | \
        cut -f 1 --complement | \
        sed 's/\.bz2/.gz/'
) > list_of_read_files.tsv