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IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
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Run IRIS on hg38 #7

Closed mguaita closed 1 year ago

mguaita commented 1 year ago

Hello,

As seen in the methods section of the paper the IRIS RNA-seq data processing uses the reference human genome hg19. Is it possible to use IRIS with the reference human genome hg38?

Also, can the IRIS functions be run individually one by one without configuring the snakemake files?

Thank you,

ypnngaa-py commented 1 year ago

Hi Maria,

We recommend using hg19 with IRIS because it has not been tested with hg38. Certain key components and steps in IRIS, such as pre-calculated databases, translation steps, and the prediction of CAR-T targets, are based on hg19.

You can run individual IRIS functions without using the full snakemake. Feel free to refer to the help manual (-h) of each function and the arguments used in the snakemake pipeline to build your own pipeline.

Yang

On Wed, May 17, 2023 at 10:26 AM Maria Guaita @.***> wrote:

Hello,

As seen in the methods section of the paper the IRIS RNA-seq data processing uses the reference human genome hg19. Is it possible to use IRIS with the reference human genome hg38?

Also, can the IRIS functions be run individually one by one without configuring the snakemake files?

Thank you,

— Reply to this email directly, view it on GitHub https://github.com/Xinglab/IRIS/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADTV3NUZTGOINSOVHW4RQ5LXGTUXNANCNFSM6AAAAAAYFILDD4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

mguaita commented 1 year ago

Hello Yang,

Thank you very much for the early reply! And, are you planning to update the pre-calculated databases and predictors to the hg38 reference?

Maria