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RNAseqTSA / TSAannotate

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Pipeline does not work #1

Open agnesfoi opened 2 years ago

agnesfoi commented 2 years ago

Dear Michael,

We have read your paper recently and found it was a very nice idea to predict neoantigen from RNA data. Thank you for your great job!

While we had some problems with our data analyze, and would like to ask for your help. For example, we can not find RData/master_input_07272021.RData from RNAseqTSA github repository, or when using gtf.load(wd), it showed that gft was missing. Could you know how to fix these bugs?

It's very important for us to test directly our RNA sequence data. We appreciate very much your help!

Sincerely yours.

michaelsharpnack commented 2 years ago

Hi there! Thank you so much for trying out our pipeline!

I agree that in its current form it is not particularly user-friendly, but hopefully I can update the code to make it easier to use with your feedback.

  1. Have you already successfully analyzed your data with TSAcore, or are you directly annotating your own peptide data with TSAannotate?
  2. I updated the github repository readme file to have more complete instructions and the rnaneoantigen.master_2.R file to be easier to customize, so pull these new changes to your local repository.
  3. You can download all of the supporting files from this dropbox link https://www.dropbox.com/sh/htkven6dl9sv0vk/AACwgJiXQVCzeOpRMyIUSXgoa?dl=0 (the link is also on github now). Note that the algorithm will default to sending your output files into this folder as well. If you load the master_input_07272021.RData file, you will not have to run the gtf.load or ccds.load functions.

Thank you again for reaching out, and please let me know if there are any more issues.

Best, Michael

On Thu, Mar 17, 2022 at 1:11 AM agnesfoi @.***> wrote:

Dear Michael,

We have read your paper recently and found it was a very nice idea to predict neoantigen from RNA data.

However, It's very difficult to analyze our data with this workflow... We lack a lot of information, such as '.Rdata' loaded, system parameters, gtf function not working, etc.

Could you please help us to figure out how to use this workflow? We appreciate very much your help!

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Yanh35 commented 1 year ago

Dear Michael, I also met the same problem when using gtf.load(wd), it showed that gft was missing. I checked the relevant code and found that "rm(gtf,gtf.mat,gtf.temp)" appeared in the sub-function of gtf.load(), but the variable gtf continued to be used later, I wonder if you can fix this problem？Also, some variables in the program are used without any assignment, such as ensLookup.

Sincerely yours.