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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
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Visualization of gene fusion from RNA seq data #1081

Closed vyomeshj209 closed 2 years ago

vyomeshj209 commented 2 years ago

Hi, Can you suggest the best way or highlight proper steps to visualize gene fusion from RNA seq data

jrobinso commented 2 years ago

Hi @vyomeshj209, could you give us more details on what type of data you have? Are you asking about alignments, or "calls" of known fusions in some other file format?

vyomeshj209 commented 2 years ago

I m trying visualize gene fusion from BAM file of sample, within it we have EWSR1--ATF1 gene fusion and specific breakpoints. What will be ideal representation that we get in IGV.

jrobinso commented 2 years ago

It depends on your purpose, there is no specific gene fusion view in IGV. If you want to look at evidence for the fusion you might turn on "show soft clips" from the Alignments preferences, you should see clipped reads at the breakpoints. The clipped portion should align to the region at the other end of the fusion. For many genomes we host you can check this by right-clicking and selecting "blat soft clip" from the menu. Finally you can view both ends at the same time using multi-locus view.

vyomeshj209 commented 2 years ago

I got soft clipped option. BLAT soft clip option is not available. It only show BLAT read sequence option. Kindly guide where to find the option.

Attaching image for reference. image.png

jrobinso commented 2 years ago

You did not state what version of IGV you are using. If theres is not blat-soft-clip options it means you either have an old version, or the read you clicked over does not have soft clips.

brainstorm commented 2 years ago

Hello @jrobinso, several of our cancer sequencing curators have noticed that this commit broke their flow with RNA fusion data analysis, perhaps is what @vyomeshj209 is also observing? Would it be possible for you to restore that particular functionality? Specifically @JoepVissers stated that:

colouring RNA reads by size and pair orientation is essential when analysing fusion genes. It helps us verify the read support for their expression.

jrobinso commented 2 years ago

@brainstorm Please open a separate issue for this, or ideally have the analysts open an issue because there will be some discussion. The commit you reference does not affect pair orientation coloring, or pairs on different chromosomes, only pair-by-insert size. The insert size stats are computed assuming DNA (no splices) so what we had before will not be restored as is, we will need to do something new appropriate for RNA.

vyomeshj209 commented 2 years ago

@jrobinso

You did not state what version of IGV you are using. If there's is not blat-soft-clip options it means you either have an old version, or the read you clicked over does not have soft clips.

1] Version used for performing the analysis -> IGV_Linux_2.9.2 2] I m getting two option for BLAT, how can we use it? Kindly guide Blat_IGV_2 Blat_IGV_1

Is it possible you to connect google met/zoom and solve these queries?

jrobinso commented 2 years ago

That's an old version, it did not have blatting of soft clips. Please update to 2.11.9. Sorry I can't give personal tutorials, and really don't have expertise in biological interpretation.

On Thu, Jan 6, 2022 at 11:30 PM Vyomesh R K Javle @.***> wrote:

@jrobinso https://github.com/jrobinso

You did not state what version of IGV you are using. If there's is not blat-soft-clip options it means you either have an old version, or the read you clicked over does not have soft clips.

1] Version used for performing the analysis -> IGV_Linux_2.9.2 2] I m getting two option for BLAT, how can we use it? Kindly guide [image: Blat_IGV_2] https://user-images.githubusercontent.com/77434374/148491778-da5304aa-f5c3-4daf-9424-660b3538c104.png [image: Blat_IGV_1] https://user-images.githubusercontent.com/77434374/148491780-5efa7cce-08df-45e1-a79c-c8309f1ecd18.png

Is it possible you to connect google met/zoom and solve these queries?

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