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alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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Usage examples in vignette #2

Closed stephenturner closed 9 years ago

stephenturner commented 10 years ago

How about some usage examples and guidance on reasonable defaults for various simulation goals to be included in the vignette?

alyssafrazee commented 10 years ago

Consider it on the to-do list! Will close issue when finished.

esterpantaleo commented 10 years ago

Trying to use the package, it looks very useful! thanks!

Found a minor correction to the manual. In the usage example of function simulate_experiment_countmat: instead of simulate_experiment_countmat(fastapath, readmat, outdir=outdir, seed=5) it should be simulate_experiment_countmat(fasta=fastapath, readmat=readmat, outdir=outdir, seed=5), otherwise the function returns:

"Error in simulate_experiment_countmat(fastapath, readmat, outdir = outdir, : must provide either fasta or both gtf and seqpath"

alyssafrazee commented 10 years ago

@esterpantaleo thanks! fixed with this commit. Also feel free to submit pull requests for this kind of thing!

alyssafrazee commented 9 years ago

The package (including the vignette and corresponding manuscript) has now undergone some major updates and has some examples / default parameters, so am closing this issue.