[khmer] Questions about abundance-dist-single.py

C. Titus Brown ctb at msu.edu
Sun Dec 22 21:13:29 PST 2013

On Sun, Dec 22, 2013 at 11:28:49PM -0500, Tamer Mansour wrote:
> I have couple questions about the "abundance-dist-single.py"
> 1) The input file: should I concatenate the single reads files to the
> interleaved paired-ended files?

Doesn't matter, but you will need everything you want to count
in a single file.

> 2) Does the '-b' option increase or decrease the chance of false positive
> results? is not recommended to be used?

-b makes the maximum count be 255.  Probably not a good idea for mRNAseq,
but probably fine for genome counting.

> 3) Does the '-savehash' option requires increasing the job resources
> (either time or ram)?

Only the time it takes to save the file to disk.

C. Titus Brown, ctb at msu.edu

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