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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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Stranded RNA-Seq #13

Closed jwcasement closed 8 years ago

jwcasement commented 10 years ago

Hello Alyssa,

I've added aditional parameters to the simulate_experiment function to enable stranded RNA-seq data to be simulated. The default option is for unstranded data (as before); additional strand-specific protocol options are 'firststrand' and 'secondstrand'.

I've also included the option to set an error rate for strandedness should this be required (default value zero).

Best regards,

John.

alyssafrazee commented 10 years ago

Thanks for the PR! I will likely be able to review it sometime next week.

alyssafrazee commented 9 years ago

I'm so sorry for the delay. The past couple months got a bit hectic and development stopped for a while, and then I had to do a major reorg of the package. Wanted to let you know that I haven't forgotten about this and will review the stranded options as soon as I can.

lpantano commented 9 years ago

Hi,

any chance this will go on? i think is a very good improvement.

nice work!

alyssafrazee commented 9 years ago

Would love to have this as a feature. I can't auto-merge the PR so will need to take time to review it, and will get to it as soon as I can. Thanks again for your patience!

alyssafrazee commented 8 years ago

Strand-specific option was added in https://github.com/alyssafrazee/polyester/pull/33 -- I hope that one added the needed functionality (and was able to merge that one without conflict). Closing this in favor of that, but feel free to reopen if it doesn't solve the problem.