backsplicing or circRNA visualization

Aarti Jajoo

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Mar 21, 2025, 12:56:02 PM3/21/25

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How to make a Sashimi plot for backspliced reads. What should be the input. If this feature does not exist, could the IGV team consider adding it, happy to collaborate. It will be very helpful for circRNA research.

Thank you,

Aarti

igv-help

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Mar 21, 2025, 5:55:38 PM3/21/25

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Sashimi plots are created from RNA-Seq bam files. See the user guide for more information.

Aarti Jajoo

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Mar 21, 2025, 7:59:35 PM3/21/25

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Yes, I can create Sashimi plot for linear splicing but I want to know how to do it for circRNA/back splicing event.

Thank you

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James Robinson

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Mar 21, 2025, 8:28:59 PM3/21/25

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If the event is recorded in your alignments you can make the plot, if it's not you can't (with IGV). "Recorded" here means alignment gaps specified with the "N" operator.

On Fri, Mar 21, 2025 at 4:59 PM 'Aarti Jajoo' via igv-help <igv-...@googlegroups.com> wrote:

Yes, I can create Sashimi plot for linear splicing but I want to know how to do it for circRNA/back splicing event.

Thank you

On Friday, March 21, 2025, igv-help <igv-...@googlegroups.com> wrote:

Sashimi plots are created from RNA-Seq bam files. See the user guide for more information.

On Friday, March 21, 2025 at 9:56:02 AM UTC-7 Aarti Jajoo wrote:
How to make a Sashimi plot for backspliced reads. What should be the input. If this feature does not exist, could the IGV team consider adding it, happy to collaborate. It will be very helpful for circRNA research.

Thank you,
Aarti

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James Robinson

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Mar 21, 2025, 8:30:13 PM3/21/25

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You probably need to look for another tool.

Aarti Jajoo

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Mar 21, 2025, 9:00:13 PM3/21/25

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ok thank you James.

Would be great to see circRNA visualization in IGV in the future.

Thanks,

Aarti

To view this discussion visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpvyE3LFgGW9DAm86VktcPq%2B2hsxr05PQ%3DWiP0T4RryQBg%40mail.gmail.com.

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