Script to summarize multiple individual depth files?

[Former user]

Hi,

I am running metabat2 on a dataset of 246 WMGS samples, and so it is very hard for me to store the sorted bam files after cross mapping all samples. Instead I am running jgi_summarize_bam_contig_depths for each individual mapping operation, and discarding the bam files. I am writing a little bash script that concatenates the depth files and sums the appropriate columns to generate a new totalAvgDepth value, but maybe you already have a script that does this?

Thanks and best wishes, Francisco

[Rob Egan]

Hello Franciso,

There should already be a script installed for you with the other metabat executables that does that:

merge_depths.pl depth1.txt depth2.txt [..]

This simple script will combine the depth files as output by jgi_summarize_bam_contig_depths into a single file.

Cheers,

Rob

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[Francisco Zorrilla]

Hi Rob,

Thanks for pointing out the script, I must have overlooked it earlier but its exactly what I need! Feel free to close the issue (not sure if I can close it since I created the issue anonymously).

Best wishes,

Francisco