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Sequencing pipeline

Project description

# RNAseq Analysis Pipeline

## Usage

Execute `` as follows:
$ python --help
Usage: seqpipe [OPTIONS]

Create read-genome matrix and compute all read alignments. Subsequently,
apply various scripts and aggregate results.

-r, --read PATH Path to read file/directory. [required]
-g, --genome PATH Path to genome file/directory. [required]
-o, --output DIRECTORY Directory to save results to.
--scripts / --no-scripts Whether to execute scripts or not.
-m, --min-read-len INTEGER Minimal read length.
-M, --max-read-len INTEGER Maximal read length.
-b, --bowtie-args TEXT Extra arguments for bowtie.
-t, --threads INTEGER How many threads to run in.
--help Show this message and exit.
This will create a `mapping_results_*` directory which contains two directories:
* `runs` stores all data related to each individual read file
* `results` contains data generated by scripts from the `scripts` folder

## Extras

Additional useful scripts are contained in `extra`.
The entry point is `` (check `python ./extra/ --help` for help).

The respective individual files are:
* ``
* map length-filtered reads against multiple genomes in succession
* ``
* visualize data obtained from sequential pipeline
* ``
* visualize differences in RNAseq expression levels over pairs of samples
* ``
* Various helper methods
* ``
* Plot various statistics

## Dependencies

* cutadapt
* fastqc
* [more info](
* bowtie2
* samtools
* [specifications](
* bedtools
* moreutils

* bash
* python
* numpy
* pandas
* seaborn
* matplotlib
* tqdm
* biopython
* pysam
* joblib
* click
* sh
* colorama

## Development notes

Create dev-builds with:
$ pip install --user -e .

Run tests using:
$ tox

Release new package as follows:
$ python sdist bdist_wheel

Project details

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