Question: Suggest Pirna Ngs Small Rna Analysis Pipelines/Workflows
1
gravatar for Rm
7.0 years ago by
Rm8.0k
Danville, PA
Rm8.0k wrote:

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 • 3.1k views
ADD COMMENTlink modified 4.4 years ago by opplatek40 • written 7.0 years ago by Rm8.0k
1
gravatar for weiwangumms
6.2 years ago by
weiwangumms10
United States
weiwangumms10 wrote:

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

ADD COMMENTlink written 6.2 years ago by weiwangumms10
1
gravatar for Mike Axtell
6.2 years ago by
Mike Axtell240
Penn State University
Mike Axtell240 wrote:

You could also try ShortStack.

https://github.com/MikeAxtell/ShortStack

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

ADD COMMENTlink written 6.2 years ago by Mike Axtell240
1
gravatar for opplatek
4.4 years ago by
opplatek40
Czech Republic
opplatek40 wrote:

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

ADD COMMENTlink written 4.4 years ago by opplatek40
0
gravatar for astrid.haase
5.8 years ago by
United States
astrid.haase0 wrote:

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

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by astrid.haase0
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