tssenrich

Calculate TSS enrichment for ATAC-seq data. (see also the ENCODE standards)

Installation

pip install tssenrich

or

pip install --user tssenrich

Usage

usage: tssenrich [-h] [--genome {hg38,hg19,mm10,</path/to/file.bed.gz>}] [--names] [--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,</path/to/file.bed.gz>}
                        genome build or path to BED file [hg38]
  --names               include sample names in output
  --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 [/opt/anaconda3/envs/tssenrich/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  |

Examples

tssenrich example.bam > score.txt

tssenrich --genome hg19 --log log.txt --memory 2 --processes 2 example1.bam example2.bam > scores.txt