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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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how to calculate relative abundance of genomes in different samples #138

Open linlin0026 opened 1 year ago

linlin0026 commented 1 year ago

Hi, thanks for maintaining this great tool! I want to calculate the relative abundance of one thousand genomes in about four hundred samples. , I am a bit confused about the reference learning file you gave. And I have not yet studied meta-analysis in-depth, so please forgive me if my questions are somewhat superficial. I am unsure whether I should put all the sample fastq files in "--coupled" or enter the BAM file, like - "bam-files my.bam" ? Thanks a lot for your help!

wwood commented 1 year ago

Hi,

Thanks for the nice words.

If you specify --coupled then you are inputting the reads, and CoverM will do the mapping for you (using minimap2 by default).

If you specify --bam-files then CoverM will calculate the coverage using the mappings that are in the BAM files you specify. This will be much faster since you have already done the mapping.

Either is fine, it just depends on what form your data currently is in.

Good luck.

linlin0026 commented 1 year ago

Thanks for your help. I will try it soon~