Calculate TSS enrichment for ATAC-seq data
Project description
tssenrich
Calculate TSS enrichment for ATAC-seq data. (see also the ENCODE standards)
Installation
pip3 install tssenrich
or
pip3 install --user tssenrich
Usage
usage: tssenrich [-h] [--genome {hg38,hg19}] [--memory <float>]
[--processes <int>] [--mapping-quality <int>]
[--samtools-path <path/to/samtools>]
[--log <path/to/log.txt>]
<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} genome build [hg38]
--memory <float> memory limit in GB [5]
--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
--log <path/to/log.txt>
path to log file
ENCODE standards:
| Genome | Concerning | Acceptable | Ideal |
| ------ | ---------- | ---------- | ----- |
| hg19 | < 6 | 6 - 10 | > 10 |
| hg38 | < 5 | 5 - 7 | > 7 |
Example
tssenrich --genome hg19 --log log.txt --memory 2 --processes 2 example.bam > score.txt
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