Comments (2)
shtoneyan
commented on August 26, 2024
Hello, I am trying to generate a report too but get an error message when I input a .txt file (e.g. this one - https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt). I was wondering if one of you know what the particular format is that we need to use for this file. Thank you!
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jmschrei
commented on August 26, 2024
The database has to be in MEME format. We had an engineer join this week who will help us clear up some of these functionality issues so hopefully this will be more flexible in the future.
from tfmodisco-lite.
Related Issues (20)
- Add MEME output from modisco motifs
- Add command to extract seqlets info in BED and FASTA format
- version for RNA sequence
- motifs.html report can be confusing
- Add negative pattern implementation for `meme` subcommand
- Add Unit tests
- Errors from MEME text parser leads to pandas.errors.EmptyDataError: No columns to parse from file HOT 1
- Need to raise an error if the attr or ohe files don't end in `.npz` or `.npy`
- `example_idx` doesnt trace back to original contribution scores HOT 1
- Center peak regions at summit in `modisco seqlet-bed` HOT 1
- `modisco meme` command does not return trimmed motifs and no negative patterns but only positive ones HOT 3
- --verbose is still rather taciturn HOT 1
- How are high absolute attribution scores defined? HOT 1
- `MergeMotifsAcrossRuns.ipynb` should account for indexes with respect to `--window`
- Prediction from low peak quality (qval) HOT 2
- Trouble constructing minimal example where motifs are found HOT 4
- Compatibility with bpnet-refactor HOT 2
- problem in tfmodisco input HOT 3
- necessity for the calling of use("pdf") HOT 5
- Generate basic report with out meme comparison HOT 12
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