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
1 maintainer
Release files for tssenrich 1.4.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| tssenrich-1.4.6.tar.gz | 37.8 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tssenrich-1.4.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 75.5 MB
Release files / tssenrich-1.4.6.tar.gz
| Download URL | tssenrich-1.4.6.tar.gz |
|---|---|
| Size | 37.8 MB |
| Tags | Source |
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Release files / tssenrich-1.4.6-py3-none-any.whl
| Download URL | tssenrich-1.4.6-py3-none-any.whl |
|---|---|
| Size | 37.8 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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