Question

identify circular RNA without reference genome

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8.9 years ago

songmm19900210 ▴ 20

Hello everybody, in general, circular RNA are identified with reference genome. now I want to identify circular RNA without reference genome, Do you have any paper recommended? Thanks a lot!

RNA-Seq • 2.5k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 8.9 years ago by songmm19900210 ▴ 20

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I think that is a good topic for a research project.

ADD REPLY • link 8.9 years ago by dario.garvan ▴ 520

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thanks 5heikki,don't need assemble? just use raw data? I need some paper to study. Do you have any paper recommended? Thanks a lot!

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.9 years ago by songmm19900210 ▴ 20

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Input is assumed to be assembled contigs/transcripts

ADD REPLY • link 8.9 years ago by 5heikki 11k

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thanks 5heikki, Do you have any assemble tools recommended? Thanks a lot!

ADD REPLY • link 8.9 years ago by songmm19900210 ▴ 20

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I think Trinity is quite popular at the moment for RNAseq.

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 8.9 years ago by 5heikki 11k

Ram · Answer 1 · 2016-01-15

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8.9 years ago

5heikki 11k

A blastn based approach I wrote some time ago..

ADD COMMENT • link updated 4.9 years ago by Ram 44k • written 8.9 years ago by 5heikki 11k