Question

Suggest Pirna Ngs Small Rna Analysis Pipelines/Workflows

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10.5 years ago

Rm 8.3k

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 • 4.2k views

ADD COMMENT • link updated 7.9 years ago by opplatek ▴ 280 • written 10.5 years ago by Rm 8.3k

score 1 · Answer 1 · 2014-08-05

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9.7 years ago

weiwangumms ▴ 10

ADD COMMENT • link 9.7 years ago by weiwangumms ▴ 10

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

ADD REPLY • link 9.3 years ago by astrid.haase • 0

score 1 · Answer 2 · 2014-08-06

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9.7 years ago

Mike Axtell ▴ 250

You could also try ShortStack.

ADD COMMENT • link 9.7 years ago by Mike Axtell ▴ 250

score 1 · Answer 3 · 2016-05-25

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7.9 years ago

opplatek ▴ 280

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 COMMENT • link 7.9 years ago by opplatek ▴ 280