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ChiLiubio / file2meco

Tranform files to the microtable object in microeco package
GNU General Public License v3.0
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Using Kraken2 Output from 16S ONT Epi2me software #23

Open abbyf1120 opened 2 months ago

abbyf1120 commented 2 months ago

Hello,

I am trying to use mpa2meco to generate a microtable from a Kraken2/Bracken abundance table generated by the 16S ONT Epi2me workflow. Although this 16S workflow utilizes Kraken2, the output generates a taxonomic assignment per read tsv file that does not seem to match the mpa format.

When I try to use mpa2eco(abund_table_genus), I receive this error.

mpa2meco(abund_file_path) Generate otu_table at Species level ... Error in [<-.data.frame(*tmp*, , i, value = "k__") : replacement has 1 row, data has 0

Is there any way I could use the file2meco package with this output to generate a microtable?

ChiLiubio commented 2 months ago

Hi. Could you please attach the file to let me have a look? Without the data, I am not sure how the error happened.

ChiLiubio commented 2 months ago

Hi. There is a large difference between its format and that the function requires. Generally, the function parses the taxonomic information like "kArchaea|pEuryarchaeota|c__Halobacteria". Especially the prefix is necessary. Otherwise the function can not identify how to assign the names to each level. I will think about how to extend the function to cover more cases.

abbyf1120 commented 2 months ago

Okay, thank you!