Package: umi-tools-csgx-b
.. image::https://user-images.githubusercontent.com/6096414/93030687-c7cf7300-f61c-11ea-92b8-102ec17ef6aa.pngUMI-tools was published inGenome Research <http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract>_ on 18 Jan '17 (open access)For full documentation seehttps://umi-tools.readthedocs.io/en/latest/Tools for dealing with Unique Molecular IdentifiersThis repository contains tools for dealing with Unique Molecular
Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell
RNA-Seq cell barcodes. Currently there are 6
commands.Theextractandwhitelistcommands are used to prepare a
fastq containg UMIs +/- cell barcodes for alignment.whitelist:Builds a whitelist of the 'real' cell barcodesThis is useful for droplet-based single cell RNA-Seq where the
identity of the true cell barcodes is unknown. Whitelist can
then be used to filter with extract (see below)extract:Flexible removal of UMI sequences from fastq reads.UMIs are removed and appended to the read name. Any other
barcode, for example a library barcode, is left on the read. Can
also filter reads by quality or against a whitelist (see above)The remaining commands,group,dedupandcount/count_tab, are used to
identify PCR duplicates using the UMIs and perform different levels of
analysis depending on the needs of the user. A number of different UMI
deduplication schemes are enabled - The recommended method isdirectional.dedup:Groups PCR duplicates and deduplicates reads to yield one read per groupUse this when you want to remove the PCR duplicates prior to any
downstream analysisgroup:Groups PCR duplicates using the same methods available throughdedup.This is useful when you want to manually interrogate the PCR duplicatescount:Groups and deduplicates PCR duplicates and counts the unique molecules per geneUse this when you want to obtain a matrix with unique molecules
per gene, per cell, for scRNA-Seq.count_tab:As per count except input is a flatfileSeeQUICK_START.md <./doc/QUICK_START.md>_ for a quick tutorial on
the most common usage pattern.If you want to use UMI-tools in single-cell RNA-Seq data processing,
seeSingle_cell_tutorial.md <./doc/Single_cell_tutorial.md>_Important update: We now recommend the use ofalevinfor droplet-based
scRNA-Seq (e.g 10X, inDrop etc).alevinis an accurate, fast and convenient end-to-end tool to go from fastq -> count matrix and  extends the UMI error correction inUMI-toolswithin a framework that also enables quantification of droplet scRNA-Seq without discarding multi-mapped reads.  Seealevin documentation <https://salmon.readthedocs.io/en/latest/alevin.html>_ andalevin pre-print <https://www.biorxiv.org/content/10.1101/335000v2>_ for more informationThededup,group, andcount/count_tabcommands make use of network-based methods to resolve similar UMIs with the same alignment coordinates. For a background regarding these methods see:Genome Research Publication <http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract>_Blog post discussing network-based methods <https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/>_.InstallationIf you're using Conda, you can use:.. code:: bash$ conda install -c bioconda -c conda-forge umi_toolsOr pip:.. code:: bash$ pip install umi_toolsOr if you'd like to work directly from the git repository:.. code:: bash$ git clonehttps://github.com/CGATOxford/UMI-tools.gitEnter repository and run:.. code:: bash$ python setup.py installFor more detail seeINSTALL.rst <./doc/INSTALL.rst>_HelpFor full documentation seehttps://umi-tools.readthedocs.io/en/latest/SeeQUICK_START.md <./doc/QUICK_START.md>_ andSingle_cell_tutorial.md <./doc/Single_cell_tutorial.md>_ for tutorials on the most common usage patterns.To get help on umi_tools run.. code:: bash$ umi_tools --helpTo get help on the options for a specific [COMMAND], run.. code:: bash$ umi_tools [COMMAND] --helpDependenciesumi_tools is dependent onpython>=3.5,numpy,pandas,scipy,cython,pysam,future,regexandmatplotlib