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STOmics / SAW

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How to get unspliced data #4

Closed jadexq closed 1 year ago

jadexq commented 2 years ago

Hi, I am trying out the test_data using stereoRun_singleLane_v4.1.0.sh. However, I failed to find the unspliced counts among the outputs. Do I need to modify stereoRun_singleLane_v4.1.0.sh to get the unspliced data? Thanks so much!!

qiqiHE93 commented 2 years ago

what does that means "unspliced data" ?

jadexq commented 2 years ago

In the Stereo-Seq paper supplementary information (on page e7) -- "Unspliced and spliced RNA for each cell were extracted from the E16.5 telencephalon with SAW." The unspliced data was then used for spatial RNA velocity analysis (Figure4 on Stereo-Seq paper page 7). Thanks so much!!

skpalan commented 1 year ago

Hi SAW team, I actually have the same question here. I looked through basically all the repos that BGI uploaded and cannot find an appropriate pipepline for generating spliced and unspliced RNA counts. I have tried using kallisto but ended up with failure to map barcodes back to cell postions. Thanks for your help in advance!

qiqiHE93 commented 1 year ago

Hi there,

Thank you for reaching out to me regarding your question about obtaining spliced and unspliced RNA counts.

I am glad to inform you that there is a solution that can help you obtain the unspliced and spliced RNA counts that you need. You can use the method provided in https://stereopy.readthedocs.io/en/latest/Tutorials/RNA_Velocity.html. The tutorial outlines the steps for performing RNA velocity analysis to study expression dynamics based on scRNA-seq data. I believe it will be helpful in your situation.

Please let me know if you have any further questions or if there is anything else I can assist you with. I hope this information helps!

Best regards,

HelloWorldLTY commented 5 months ago

I have the same question here. How to access the gef or bgef here? I cannot find these files. It will be really helpful if you can provide the loom file for us. Thanks.

AritaZ-hang commented 2 months ago

lol now I meet the same situation. I hope the SAW team could add a new function to add a barcode tag or bin tag whatever(like others mentioned in another issue, CB50, CB500, indicating a mapping relationship between the bead and the spatial clusters. I've tried to find such an API in the stereopy but it seems there's no such thing) . Though coordinates could be translated into barcode names by the ST_BarcodeMap tool, it's still inconvenient to directly conduct any analysis relevant to the barcode tag.