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Query sequence coverage for treesapp abundance #88

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cmorganl opened this issue Jul 8, 2021 · 1 comment
Open

Query sequence coverage for treesapp abundance #88

cmorganl opened this issue Jul 8, 2021 · 1 comment
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feature request A request for a new feature unlike one that already exists

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@cmorganl
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cmorganl commented Jul 8, 2021

treesapp abundance calculates TPM or FPKM for entire query sequences. The depth of coverage, however, is unknown.

A new feature that reports the pile-up along each query sequence's length would be valuable in determining whether specific regions of query sequences (e.g. active sites) are actually covered or not.

A new field in the classifications.tsv file could report the percentage of a query sequence that was covered and a new BED table could report the depth across each character position.

@cmorganl cmorganl added the feature request A request for a new feature unlike one that already exists label Jul 8, 2021
@cmorganl
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In order for the alignments to work the full-length nucleotide ORFs should be written to the output directory as well. Sequences should be separated into FASTA files based on the reference packages they matched.

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Labels
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