Sashimi plot visualisation

[VARRHO]

Hi everyone, 

I recently download IGV (2.12.2) in order to realise a sashimi plot. 

I am not using genome avaible on the IGV, so i Needed to upload my own (FASTA file) and a annotation track (.gbk file).

I then upload my alignment (.sam file) and try to make a shimi plot.

Sadly it didnt work and no arcs are visible :

Could someone explain me where did i made a mistake and how to fix it ? 

Thanks, 

Clément

[igv-help]

Hi Clément,

It's hard to tell what's going on just from this screenshot. First, is this RNA-seq data? Does the alignment track show evidence of splice junctions that should be represented in the Sashimi Plot?

Helga

[Clément Dominguez Lafage]

Hi, 

Yes, data are from an RNA-Seq. Actually you are right i think my sam file does not contain any splice junction... even if it should have splice junction

Does it mean that the problem come from my alignement ?

Thank you, 

Clément.

[igv-help]

The sashimi plot visualizes splices, so if there are none in the file you will see nothing on the sashimi plot.     Does it look like this everywhere in your file?  

We can't advise you on aligners, you might seek help at a more general forum like Seq Answers or biostars, or a forum for the alignment tools you are using.