circRNA reads on IGV

[gnilihzeux]

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

[Kevinzjy]

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

[gnilihzeux]

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]

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]

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