abundance histogram output from normalize-by-median

[chuckpr]

It would be nice to get the output that abundance-dist gives without having to call abundance-dist (or abundance-dist-single). E.g. could normalize-by-median output the k-mer count information to make a k-mer abundance histogram?

[ctb]

On Sun, Apr 06, 2014 at 04:00:53AM -0700, chuckpr wrote:

It would be nice to get the output that abundance-dist gives without having to call abundance-dist (or abundance-dist-single). E.g. could normalize-by-median output the k-mer count information to make a k-mer abundance histogram?

Unfortunately, no. Both abundance-dist and abundance-dist single require
the allocation of additional memory and another pass across the data, neither
of which fit within normalize-by-median's remit (or are good ideas for large
data sets :)

--t

C. Titus Brown, ctb@msu.edu

[ctb]

On Sun, Apr 06, 2014 at 04:00:53AM -0700, chuckpr wrote:

It would be nice to get the output that abundance-dist gives without having to call abundance-dist (or abundance-dist-single). E.g. could normalize-by-median output the k-mer count information to make a k-mer abundance histogram?

Note, however, that the 'savetable' from normalize-by-median can be used as
input into abundance-dist. This should be added to the docs.

[mr-c]

Fixed by f4efd19