From dcdf6b6ba82a7a5e2d2e04068fb90f51651085b4 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 14 Jul 2026 14:51:22 -0400 Subject: [PATCH 1/2] Update average.md Updated the prepare documentation to include: A description of the --genome argument A description of the --max_zooms argument Also alphabetized optional arguments. --- docs/readme/average.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/docs/readme/average.md b/docs/readme/average.md index e0b4d78..85c6c28 100644 --- a/docs/readme/average.md +++ b/docs/readme/average.md @@ -28,22 +28,27 @@ The name string used to build the output filename. The extension `.bw` will be a ## Optional Arguments -### `-cs`, `--chrom_sizes`, `--chromosome_sizes` - -The chromosome sizes file for the reference genome used during alignment. The current default is set for hg38. - ### `-c`, `--chroms`, `--chromosomes` -The chromosomes that are averaged together and written to output. Only the chromosomes in this list will be written to the output file. The current default list of chromosomes are restricted to the autosomal chromosomes: +The chromosomes that are averaged together and written to output. Only the chromosomes in this list will be written to the output file. The current default list of chromosomes are restricted to the human autosomal chromosomes: ```bash chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 ``` -### `-o`, `--output`, `--output_dir` +Note: this argument MUST be specified in conjunction with `--genome` and `--chrom_sizes` if the input file was aligned to a genome build other than hg38. + +### `-cs`, `--chrom_sizes`, `--chromosome_sizes` + +The chromosome sizes file for the reference genome used during alignment. The current default is set for hg38. Note: this argument MUST be specified in conjunction with `--genome` and `--chromosomes` if the input file was aligned to a genome build other than hg38. -The output directory. If the output directory is not supplied the file will be created in the current working directory. +### `--max_zooms` +The number of zoom levels that should be computed for the normalized bigWig file. Zoom levels are pre-computed summary statistics that enable fast zooming into/out of a genomic region in a bigWig file when a visualization tool (e.g., IGV, UCSC Genome Browser). Lower values of this parameter result in slower loading of bigWig files in visualization tools, while higher values of this parameter result in a large memory overhead. The range of potential parameter values is (0-10). Default: 5. Note: if this argument is set to 0, the resulting bigWig files are NOT compatible with other bigWig tools (e.g., deepTools) and cannot be visualized using tools like IGV and the UCSC Genome Browser. Please see: https://github.com/deeptools/pyBigWig/blob/master/README.md for additional details. ### `--loglevel` Set the logging level. Currently, the only working logging level is `ERROR`. + +### `-o`, `--output`, `--output_dir` + +The output directory. If the output directory is not supplied, the file will be created in the current working directory. From 9eda2103dd5bd06e9f566b177b1707d02979088e Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 14 Jul 2026 15:20:24 -0400 Subject: [PATCH 2/2] Update average.md --- docs/readme/average.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/readme/average.md b/docs/readme/average.md index 85c6c28..d3a6189 100644 --- a/docs/readme/average.md +++ b/docs/readme/average.md @@ -43,7 +43,7 @@ Note: this argument MUST be specified in conjunction with `--genome` and `--chro The chromosome sizes file for the reference genome used during alignment. The current default is set for hg38. Note: this argument MUST be specified in conjunction with `--genome` and `--chromosomes` if the input file was aligned to a genome build other than hg38. ### `--max_zooms` -The number of zoom levels that should be computed for the normalized bigWig file. Zoom levels are pre-computed summary statistics that enable fast zooming into/out of a genomic region in a bigWig file when a visualization tool (e.g., IGV, UCSC Genome Browser). Lower values of this parameter result in slower loading of bigWig files in visualization tools, while higher values of this parameter result in a large memory overhead. The range of potential parameter values is (0-10). Default: 5. Note: if this argument is set to 0, the resulting bigWig files are NOT compatible with other bigWig tools (e.g., deepTools) and cannot be visualized using tools like IGV and the UCSC Genome Browser. Please see: https://github.com/deeptools/pyBigWig/blob/master/README.md for additional details. +The number of zoom levels that should be computed for the averaged bigWig file. Zoom levels are pre-computed summary statistics that enable fast zooming into/out of a genomic region in a bigWig file when a visualization tool (e.g., IGV, UCSC Genome Browser). Lower values of this parameter result in slower loading of bigWig files in visualization tools, while higher values of this parameter result in a large memory overhead. The range of potential parameter values is (0-10). Default: 5. Note: if this argument is set to 0, the resulting bigWig files are NOT compatible with other bigWig tools (e.g., deepTools) and cannot be visualized using tools like IGV and the UCSC Genome Browser. Please see: https://github.com/deeptools/pyBigWig/blob/master/README.md for additional details. ### `--loglevel`