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doc: Fixed column id and hmmlearn version #3

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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -3,7 +3,7 @@
- **pandas**
- **numpy**
- **getopt**
- **hmmlearn** (version: 0.2.5)
- **hmmlearn** (required version: 0.2.5)
- **pyarrow**
- **pytables**
- **pickle**
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- **Optional Parameters:**
- `-l` Minimum footprints allowed per read (default: 0).
- `-r` Enable circular mode (default: off).
- `-b` Column number (0-based) in BED files with reference methylation starts (e.g., 12 for m6A output from fibertools, 28 by default for full output).
- `-b` Column number (0-based) in BED files with reference methylation starts (e.g., 11 for m6A output from fibertools, 28 by default for full output).
- `-s` Chunk size (default: 50000).
- `-e` How many bases to mask on both ends of the read as 0% methylation probability (default is 10). Required due to the fact that fibertools needs a window to call methylations.
- `-m` Minimum fraction of methylations required in a read (default: 0).
Expand All @@ -72,7 +72,7 @@ The repository includes a folder `Example files` containing necessary files to r
### Input Files
- **accessible_probs.tsv** and **inaccessible_probs.tsv** – probability files for accessible and inaccessible regions (`-p` parameter).
- **dm6.fa** – *Drosophila melanogaster* (dm6) reference genome in FASTA format. This file is too large for github, so please download the file yourself.
- **dm6_example.bed** – example FiberHMM m6A-only output file for m6A modifications. You should specify `-b 12` to use the correct column.
- **dm6_example.bed** – example FiberHMM m6A-only output file for m6A modifications. You should specify `-b 11` to use the correct column.

### Expected Output Files
- **dm6_example_model.pickle** – trained model for the example dataset.
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