Comments (13)
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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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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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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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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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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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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Related Issues (13)
- incomplete warning message HOT 1
- running for a long time; output stopped in the middle of a warning HOT 12
- "-g" in prep? exists in README.md, but not usage message HOT 2
- Possible to upgrade to latest numpy? HOT 3
- Error when running Neoepiscope HOT 2
- Support substitutions longer than 1
- Python 2 and 3 order transcripts in output differently HOT 1
- Transcript.py expressed edit function has list index problems during edits out of interval ranges HOT 1
- Integrating HapCUT2 HOT 2
- No neoepitopes found. HOT 7
- Prioritizing neoepitopes HOT 2
- transcript_to_gene_info.pickle is not loaded HOT 1
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