diff --git a/README.md b/README.md index 3ed941a..b13c103 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ - **pandas** - **numpy** - **getopt** -- **hmmlearn** (version: 0.2.5) +- **hmmlearn** (required version: 0.2.5) - **pyarrow** - **pytables** - **pickle** @@ -54,7 +54,7 @@ - **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). @@ -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.