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

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