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Old 03-07-2012, 05:20 PM   #1
calmac3
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Location: Austin, TX

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Default easyRNASeq

This dev package looks very promising to simplify read summaries. I'm sorry if I missed this in the documentation, but I am wondering how the package handles paired-end reads. I have a dataset with a mixture of paired- and single-end reads. How does this impact the "readLength" line?

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Old 03-21-2012, 05:25 PM   #2
calmac3
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I suppose I will answer my own question. At this point, without input from the developers, do not try to mix paired-and single-end reads.
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Old 09-20-2012, 08:46 AM   #3
regyre
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Hi Calmac3,

The best place to get an answer about Bioconductor packages is the bioconductor mailing list. I honestly would not have expected posts about easyRNASeq here on SEQanswers.

To answer your question: if you use version 1.2.5 of easyRNASeq, there's no support for PE. If you use 1.3.14, you do not need to provide the readLength argument as this information will be extracted directly from your data. Concerning the PE data, they are still considered as SE as I'm working on a proper way to define/count fragments and not reads. I hadn't thought of mixed SE-PE setup but will keep that in mind. If you have other questions, or suggestions, comments, please post on the Bioc mailing list. At list you'll get a quicker answer!

Nico
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