Question

identify circular RNA without reference genome

2

Entering edit mode

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 2.4 years ago by Ram 44k • written 8.9 years ago by songmm19900210 ▴ 20

1

Entering edit mode

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

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

0

Entering edit mode

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 5.0 years ago by Ram 44k • written 8.9 years ago by songmm19900210 ▴ 20

1

Entering edit mode

Input is assumed to be assembled contigs/transcripts

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

0

Entering edit mode

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

ADD REPLY • link 8.9 years ago by songmm19900210 ▴ 20

0

Entering edit mode

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

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 8.9 years ago by 5heikki 11k

Ram · Answer 1 · 2016-01-15

3

Entering edit mode

8.9 years ago

5heikki 11k

A blastn based approach I wrote some time ago..

ADD COMMENT • link updated 5.0 years ago by Ram 44k • written 8.9 years ago by 5heikki 11k