Issue with analysis of splice junctions

[neha dinesh]

Hi,

 I’m Neha from Reinhardt lab at McGill and I’m writing today regarding some technical aspects with IGV.

I have RNA-seq data wherein I’m interested in analyzing splice junctions and make sashimi plots for a particular gene of interest.

Unfortunately when I load tracks I don’t get the options to visualize for neither the splice junctions or even how to make sashimi plots (image below).

I followed  the online tutorials from IGV but seems like the downloaded version I have on my desktop doesn’t have these feature.

 

Can someone please clarify what is the issue here.

 

Thank you

Neha

 

[igv-help]

Hi Neha,

You forgot to include the image, but I happened to see it in the email you sent to igv-team.

The sashimi plot is a feature of the alignment track - but I don't see that you loaded any RNA-seq data.

I only see the refseq gene track and a bigwig track.

Helga

[neha dinesh]

Hi Helga,

Thank you for the response.

What would you mean by RNA seq data? We got assistance from the Canadian computational genomics centre of canada to help with analysis of RNA seq data and in the output files they provided us with DEG file and bigwig files. They told us that the bigwig files would be enough for looking at the splice reads.  What files would i require for the analysis I'm looking for?

Thank you 

Neha

[igv-help]

The IGV Sashimi Plot uses as input the aligned reads from the sequencing. The file would be in .bam or .cram format, and would be accompanied by a corresponding index file (.bai or .crai). Perhaps they can give you those files. Or perhaps they have suggestions for how to view the files they already sent you.

[neha dinesh]

OK great thank you so much Helga. That helps a lot.

Best

neha 

[neha dinesh]

Hi,

Can someone please help me understand why some reads have red and blue stretches on IGV.

Images attached.

Thank you

Neha 

[igv-help]

See this:  https://software.broadinstitute.org/software/igv/interpreting_insert_size