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maryawood avatar maryawood commented on August 23, 2024

Hello, I'm sorry that you are having trouble! I have requested access to your google drive folder so I can take a look at the data and try to see what the problem is.

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alex84425 avatar alex84425 commented on August 23, 2024

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maryawood avatar maryawood commented on August 23, 2024

Thank you, I am able to access the folder now! The file names in that directory do not match the ones you use in the commands. Could you tell me which file names in the google drive folder correspond to the file names in your commands?

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alex84425 avatar alex84425 commented on August 23, 2024

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alex84425 avatar alex84425 commented on August 23, 2024

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maryawood avatar maryawood commented on August 23, 2024

Which version of neoepiscope did you use for your analysis? The software should be able to handle cases where there are multiple alternate alleles as you described, but I would like to test out the commands using the same version as you so I can better see what happened

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alex84425 avatar alex84425 commented on August 23, 2024

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alex84425 avatar alex84425 commented on August 23, 2024

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maryawood avatar maryawood commented on August 23, 2024

Sorry for the delay, I had not had a chance to work on this yet! I just took a look today, and as suspected I got a similar error whether or not I retained variants with multiple alternate alleles. It appears that the issue is actually variants with '*' as the alternate allele, representing spanning deletions, which neoepiscope does not currently support. Thank you for bringing this to our attention! We will plan to incorporate a fix for this into an upcoming release of neoepiscope to increase the flexibility of the tool.

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alex84425 avatar alex84425 commented on August 23, 2024

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maryawood avatar maryawood commented on August 23, 2024

No bother at all! We don't currently have built-in support for genomes other than human hg19/hg38, but it's pretty easy to get things set up on your own to use a different genome/species. Instead of using the --build option when running neoepiscope call, you will use the --dicts and --bowtie-index options with some data you download (and process a bit) yourself.

If you'd like to use a mouse model instead of a human model, you can download the mouse GTF file for your genome build of choice from GENCODE: https://www.gencodegenes.org/mouse/

Using neoepiscope index, you can then index the GTF file to create pickled dictionaries necessary for predicting neoepitopes. This only needs to be done once. Then whenever you run neoepiscope call, you can use the --dicts option on the command line to specify the directory containing those pickled dictionaries.

Additionally, you will need a bowtie index for your mouse genome, which you can download from the bowtie website: ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/

You can use this index with the --bowtie-index option when running neoepiscope call

Hope this helps!

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alex84425 avatar alex84425 commented on August 23, 2024

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maryawood avatar maryawood commented on August 23, 2024

Thank you for the suggestion! That is something that we will probably add in the future. Also, the latest release of neoepiscope should be able to handle the spanning deletions you had issues with before, so hopefully that will no longer cause problems for you if you update your installation of neoepiscope!

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