NAME

fasda normalize - Normalize abundances given raw counts and lengths

SYNOPSIS

fasda normalize abundance1.tsv abundance2.tsv ...

OPTIONS

--mrn

Use Mean Ratios Normalization [default]

DESCRIPTION

The fasda normalize command attempts to normalize the read counts in 2 or more kallisto-style abundance.tsv files. Each TSV file represents a biological sample. Multiple samples are required in order to statistically estimate the normalization factor.

Currently, only Median Ratios Normalization (MRN) is implemented. This method computes the average count for all samples of a given feature (e.g. gene or transcript), then the ratio of each count to the average for the feature, and finally the median ratio for each sample. The median ratio is the scaling factor for that sample. This should, in theory, normalize for differences in library size (total reads for a given sample). This method assumes that technical effects are the same for DE and non-DE genes and that expression is roughly symmetric (there are equal numbers of up-regulated and down-regulated genes). [Evans, et al, 2018 doi: 10.1093/bib/bbx008]

Additional normalization methods, including the use of spike-in controls, are planned for the future.

FILES

abundance.tsv - kallisto-style abundance estimates

SEE ALSO

fasda-abundance(1), fasda-fold-change(1)

BUGS

Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR

J. Bacon