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Suggest Pirna Ngs Small Rna Analysis Pipelines/Workflows

I have small RNA sequencing reads generated using NEB kit. I have tried proTRAC workflow, but not much success.

I need your suggestions for the alternate tools or analysis workflows to detect and analyze piRNAs from NGS data.

workflow
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updated by opplatek opplatek • written by Rm Rm

3 answers

please try piPipes. https://github.com/bowhan/piPipes

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written by weiwangumms • weiwangumms

concerning piPipes: can i use also the RNAseq pipeline (transcriptome) with single-end reads?

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written by astrid.haase • astrid.haase

You could also try ShortStack.

https://github.com/MikeAxtell/ShortStack

http://www.ncbi.nlm.nih.gov/pubmed/23610128

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written by Mike Axtell Mike Axtell

You can also try Kraken which has a specific part of pipeline just for piRNA analysis (see examples) http://www.ebi.ac.uk/research/enright/software/kraken

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written by opplatek opplatek

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