Sashimi plots always without arcs

[jam.v...@gmail.com]

Hello,

I've used IGV for quite some time now for all kinds of sequencing data, however I've never managed to get the Sashimi plot or junction track functions to work with RNAseq data.

We're currently looking at Oxford Nanopore reads and I would really like to use the Sashimi plots to show novel splice junctions in this data.

As an example I've taken a subset of reads from the most recent run and tried to create Sashimi plot or splice junction tracks. There are reads which clearly span across the exon-intro junctions in this example, however no junctions are created in the plot for neither the refseq annotation nor the gencode v19 annotation.

Does anyone know what I'm doing wrong, is it something that's not encoded in the BAM files? In this case they were aligned using minimap2 and sorted with picard, but I've seen this same behaviour with STAR-2-pass.

Best regards and thanks in forward,

Joost Verlouw

[jam.v...@gmail.com]

[James Robinson]

How are the junction gaps tagged in the cigar string of your BAM file?   From you BAM screenshot it looks like they are tagged as deletions ("D" operator),  not junctions ("N" operator).  

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/79ef3b28-808a-45ff-898e-259fe0e0ef6a%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.