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bioinfo-biols / CIRI-long

Circular RNA Identification for Nanopore Sequencing
https://ciri-cookbook.readthedocs.io
MIT License
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circRNA reads on IGV #16

Open gnilihzeux opened 2 years ago

gnilihzeux commented 2 years ago

Hi, is there any option to save mapped reads? So, we could display the circRNA reads on IGV.

Kevinzjy commented 2 years ago

I am afraid not, the current version of CIRI-long does not generate reads alignment results.

gnilihzeux commented 2 years ago

So, whether if I could generate those using your strategy in the paper ?

Cleaned reads were aligned to the mouse genome (GRCm38) version M20 (Ensembl 95) using minimap2 (ref. 45)
with the ‘–x splice’ option.

BTW, is it a better option using sequences in xxx.cand_circ.fa instead of cleaned reads ?

Thanks.

Kevinzjy commented 2 years ago

Yes, you could use minimap2 to align cand_circ.fa to the reference genome. The result should be slightly different from the final collapsed output, but should still be enough for visualizing circRNA isoforms.

gnilihzeux commented 2 years ago

Well, it might be better if I just use reads in xxx.reads to align xxx.cand_circ.fa to the reference genome.