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user question: can we get the k-mer counts per input sample? #6

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ctb opened this issue Jul 2, 2020 · 0 comments

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ctb commented Jul 2, 2020

question:

Does your pipeline have a way to output k-mer signature matrices (k-mer counts per input sample)? We can only seem to pull out the pairwise similarity matrices between samples.

answer from taylor:

The counts per sample information is located in the output folder: outputs/filt_sigs_named_csv.
There is one CSV per sample, and these are unnormalized counts.

There is also a normalized count matrix here: "outputs/hash_tables/normalized_abund_hashes_wide.feather"
It's in feather format, so you can either use the python or R libraries to read the file into a dataframe. I think the function is read_feather() for both libraries.

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