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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Normalize the abundance data #276

Closed mars188 closed 2 weeks ago

mars188 commented 5 months ago

Hello,

I ran rgi main for genome assemblies as below:

rgi main -i sample1.fasta -o sample1 -a DIAMOND -n 24 --clean

Then I ran rgi heatmap as below:

rgi heatmap -i json_files -o hm_output -clus both -f

Along with heatmap, it also produced a csv file with gene count or frequency.

Next, I want to normalize these genecounts with RPKM approach. Can you please suggest me how to do it? Or if there is inbuilt function in rgi for this purpose?

Many thanks in advance!

github-actions[bot] commented 3 months ago

Issue is stale and will be closed in 7 days unless there is new activity

github-actions[bot] commented 3 weeks ago

Issue is stale and will be closed in 7 days unless there is new activity