Paired-End Protocol For Micrornaseq
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11.0 years ago

In Mirna-Seq Trimming And Mapping?, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.

I never heard about a paired-end protocol for miRNAseq and would be interested in some more information. Does anyone know this protocol?


My questions would be:

  • Since the reads from mature miRNAs are very short, do the two pairs completely overlap with each other?
  • Is this protocol still strand specific? Is the first mate always the one on the correct strand?
  • I don't think that recent tools like miRDeep, or miRanalyzer can handle this information. Are there tools which can?
  • ...

I would be really thankful for some input! :)

ngs paired-end • 2.9k views
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i dont think paired end is even necessary for miRNAs or other small RNAs (paired end was invented for sequencing longer regions)

miRDeep uses bowtie for alignment. So you can just open the mirdeep code and modify it to run bowtie in a different mode (another one line of script can be used to combine the mates.)

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