multiple methods in a single run

[xinehc]

Hello,

Does coverM currently support multiple methods (e.g. mean + variance) as output?

Thanks!

for method in rpkm coverage_histogram relative_abundance mean variance
do
    coverm genome --bam-files $bam \
        --genome-fasta-directory mags \
        --genome-fasta-extension fa \
        --methods $method \
        --threads 20 \
        --output-file coverage/$method.tsv
done

[wwood]

Hi, Yes it can. In fact there's no need for a for loop. Just use coverm genome -m rpkm relative_abundance .... The exception is coverage histogram since the shape of the output is different. To save mapping CPU time, you could use use a bam cache. HTH, ben -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

…

________________________________ From: Xi Chen ***@***.***> Sent: Friday, June 3, 2022 6:17:58 PM To: wwood/CoverM ***@***.***> Cc: Subscribed ***@***.***> Subject: [wwood/CoverM] multiple methods in a single run (Issue #119) Hello, Does coverM currently support multiple methods (e.g. mean + variance) as output? Thanks! for method in rpkm coverage_histogram relative_abundance mean variance do coverm genome --bam-files $bam \ --genome-fasta-directory mags \ --genome-fasta-extension fa \ --methods $method \ --threads 20 \ --output-file coverage/$method.tsv done ― Reply to this email directly, view it on GitHub<#119>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5CDG3SYMKDUFUKVMRLVNG5TNANCNFSM5XXXVRTA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>