scbs 0.6.0

command line tool for the analysis of single-cell bisulfite-sequencing data

scbs: A Command Line Tool for the Analysis of Single-Cell Bisulfite-Sequencing Data

Installation

You can install scbs from the Python package index as follows:

python3 -m pip install --upgrade pip  # you need a recent pip version
python3 -m pip install scbs

Then restart your terminal. The installation is now finished and the command line interface should now be available when typing the command scbs in your terminal. If this is not the case, check the "troubleshooting" section below.

Updating to the latest version

Just use --upgrade when installing the package, otherwise it's the same process as installing:

python3 -m pip install --upgrade scbs

Afterwards, make sure that the latest version is correctly installed:

scbs --version

Tutorial of a typical scbs run

A tutorial can be found here.

Also make sure to read the help by typing scbs --help or by checking this page.

What can this package do?

scbs takes as input a number of single-cell methylation files and allows you to quickly and easily obtain a cell × region matrix for downstream analysis. It also facilitates quality control, allows you to discover variably methylated regions (VMRs), accurately quantifies methylation in genomic intervals, and stores your sc-methylomes in an efficient manner.

You can find a list of the available scbs commands here.

bioRxiv preprint

For a detailed explanation of the methods implemented in scbs, please check our bioRxiv preprint:

Analyzing single-cell bisulfite sequencing data with scbs
Lukas PM Kremer, Leonie Kuechenhoff, Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders
bioRxiv 2022.06.15.496318; doi: https://doi.org/10.1101/2022.06.15.496318

Troubleshooting

Installation issues

Carefully check the output log of PIP. Look for a message like WARNING: The script scbs is installed in '/home/ubuntu/.local/bin' which is not on PATH., which would indicate that you need to add /home/ubuntu/.local/bin to your path. Alternatively, you can copy /home/ubuntu/.local/bin/scbs to e.g. /usr/local/bin.

If you encounter other problems during installation, make sure you have Python3.8 or higher, and make sure you have the latest PIP version. If the problem persists, consider installing scbs in a clean Python environment (for example using venv).

Too many open files

If you encounter a "too many open files" error during scbs prepare (OSError: [Errno 24] Too many open files), you need to increase the maximum number of files that can be opened. In Unix systems, try ulimit -n 9999.

Contributors

• Lukas PM Kremer
• Martina Braun
• Leonie Küchenhoff
• Alexey Uvarovskii
• Simon Anders