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How to profile results only identify 1 species per reference #44
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Hi Phuc, Thanks for using KMCP.
You might add the output in CAMI format, where the abundance of each rank is provided.
Or MetaPhlan format, which might have more downstream analysis tools.
You can add
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Thanks Shenwei, but it seems my intended use is a bit more complicated
I want to further use taxpasta after profiling with KMCP but currently taxpasta only supports main output of KMCP and I have tried using CAMI and MetaPhlan format output from KMCP but taxpasta gives an error so I am aiming to use KMCP's
I tried using
-> There are 2 refs per Schaalia odontolytica with approximately the expected number of reads
-> There is only 1 ref per Schaalia odontolytica but the number of target reads has been decreased
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I think the fastest way is to write a script to add the read count information of minor strains to the dominant strain for each species. You can write it by yourself, or wait for me for a few days cause I'm busy recently.
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Thank you very much, I'll try to complete it on my own, but if you have the time, I think it will be really helpful for others who have the same purpose as me. I will also feel more secure when using that script because it is highly credible since it was written by you. Thank you for your great support Shenwei |
I assume that you only need the accumulated sum of reads for each species. Please download the latest versions of csvtk and taxonkit. We need the speciess name (not the column
Add species names
Add the reads numbers for all species
Keep one reference for each species and update the reads number
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Thank you very much Shenwei, I will try using the method you instructed to process the output table from KMCP and perform the downstream analysis steps to see if everything is okay. I sincerely appreciate your passionate support. |
Dear Shenwei,
Thank you very much for providing a good tool, I am trying to adjust the output table as desired according to KMCP format.
Thank you so much,
Best,
Phuc
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