计算atac seq数据的tss富集度
tssenrich的Python项目详细描述
tssenrich
为atac seq数据计算TSS enrichment。（另请参见ENCODE standards）
安装
pip3 install tssenrich
或
pip3 install --user tssenrich
用法
usage: tssenrich [-h] [--genome {hg38,hg19,mm10}] [--memory <float>]
[--processes <int>] [--mapping-quality <int>]
[--samtools-path <path/to/samtools>]
[--log <path/to/log.txt>] [--tmp-dir <temp/file/dir/>]
[--flank-distance <int>] [--flank-size <int>]
<path/to/file.bam> [<path/to/file.bam> ...]
calculate TSS enrichment for ATAC-seq data
positional arguments:
<path/to/file.bam> Path to input BAM file
optional arguments:
-h, --help show this help message and exit
--genome {hg38,hg19,mm10}
genome build [hg38]
--memory <float> memory limit in GB [2]
--processes <int> number of processes/threads to use [1]
--mapping-quality <int>
ignore reads with mapping quality below the given value [0]
--samtools-path <path/to/samtools>
path to an alternate samtools executable [/usr/local/bin/samtools]
--log <path/to/log.txt>
path to log file
--tmp-dir <temp/file/dir/>
directory to use for temporary files
--flank-distance <int>
distance from tss of outer ends of flanks [1000]
--flank-size <int> size of flanks (for determining average depth) [100]
ENCODE standards:
| Genome | Concerning | Acceptable | Ideal |
| ------ | ---------- | ---------- | ----- |
| hg19 | < 6 | 6 - 10 | > 10 |
| hg38 | < 5 | 5 - 7 | > 7 |
| mm10 | < 10 | 10 - 15 | > 15 |
示例
tssenrich example.bam > score.txt
tssenrich --genome hg19 --log log.txt --memory 2 --processes 2 example1.bam example2.bam > scores.txt
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