quant

Pseudo-quantification of expression of a set of query sequences against a Malva Index

usage: malva quant [-h] [--index-in INDEX_IN] [--reference REFERENCE] [--background-model BACKGROUND_MODEL] --folder-out FOLDER_OUT [--h5ad] [--bin-size BIN_SIZE] [--sliding-size SLIDING_SIZE]
                   [--pct-threshold PCT_THRESHOLD] [--kmer-min KMER_MIN] [--kmer-max KMER_MAX] [--single-count]

Named Arguments

--index-in

Valid directory where the malva index (and metadata) is located.

The directory must contain the file malva_index.h5. Otherwise, an exception will be thrown.

--reference

Reference used for pseudoquantification. Options available: ‘human_utr’, ‘human_cdna’, ‘human_markers’, ‘human_markers_hallmarks’, ‘human_utr_ncrna’, ‘human_cdna_ncrna’, ‘mouse_utr’, ‘mouse_markers’, ‘mouse_cdna’, ‘mouse_utr_ncrna’, ‘mouse_cdna_ncrna’, ‘drosophila_markers’, ‘arabidopsis_markers’. Default: ‘human_utr’

Default: 'human_utr'

--background-model

Path to background model (*.bmodel.bin) of k-mer abundance (those too abundant will be ignored during query, e.g., multimappers). Default: None

--folder-out

Directory where the gene expression pseudoquantification.

Three files will be created, similar to cellranger output: barcodes.txt.gz, features.txt.gz, and matrix.mtx

--h5ad

When specified, Resaves matrix.mtx to AnnData format, at –folder-out.

Default: False

--bin-size

Aggregates spatial units from the AnnData file into bins (when –h5ad is specified). Default: 0 (no binning)

Default: 0

--sliding-size

Quantification sliding window size; should match average indexed read length. Default: 128

Default: 128

--pct-threshold

Percentage of indexed k-mers (0-1 range) that should match per coordinates for considering match. Default: 65 (percent)

Default: 0.65

--kmer-min

k-mers occurring less than –kmer-min times are ignored

Default: 10

--kmer-max

k-mers occurring more than –kmer-max times are ignored

Default: 10000

--single-count

When specified, malva counts whether the query sequence was found or not

for a specific sequence.

Default: False