/bskim-2015-pre-miRNA

Supplementary data for Kim et al. (2015), a TUT4/7 paper from the V. Narry Kim lab.

Primary LanguagePython

Supplementary Data for Boseon Kim et al. (2015)

by Hyeshik Chang <hyeshik@snu.ac.kr>

See Article: B. Kim, M. Ha and L. Loeff et al. (2015) TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms. EMBO Journal. in press

(c) Boseon Kim

This repository includes scripts and interactive notebooks for the data analysis of the high-throughput sequencing of pre-miRNAs in HeLa cells. See the supplementary experimental procedures included in the manuscript for the detailed descriptions of the analytic processes.

Saved notebook sessions

  1. Modification frequency throughout the 3' end positions of templated nucleotides
  2. Bird's eye view for 3' end and uridylation patterns in control and TUT247 knockdown samples
  3. Global change of uridylation by knockdown of TUT2/4/7
  4. Relationships between 3' end trimming and uridylation?

Availability of the sequencing data

You can download the FASTQ files enclosing the reads from pre-miRNA sequencing from the NCBI Gene Expression Omnibus (GEO) with an accession number GEO64482.

Prerequisites

Instructions

  1. Check out the repository.

    $ git clone https://github.com/hyeshik/bskim-2015-pre-miRNA.git
$ cd bskim-2015-pre-miRNA

  2. Run the pipeline.

    $ snakemake -j

Using a Docker image

In alternative to install the prerequisites into your machine, you can use our Docker image to replicate our analysis.

  1. Launch a container after pulling an image from the Docker hub.

    $ docker run -t -i hyeshik/bskim-2015:r1 /bin/bash

  2. Run the pipeline.

    # cd /home/hyeshik/bskim-2015-pre-miRNA; snakemake -j

The MIT License

Copyright (c) 2014 Hyeshik Chang

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.