A pipeline for profiling TE-derived small RNAs.
Created by Wen-Wei Liao, Kat O'Neill & Molly Hammell, March 2017
Install Miniconda 3 (Linux)
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh
$ conda config --add channels conda-forge $ conda config --add channels bioconda
$ git clone https://github.com/mhammell-laboratory/TEsmall.git $ cd TEsmall $ conda env create -f environment.yaml -n TEsmall $ conda activate TEsmall $ python setup.py install
How to run TEsmall
Before executing TEsmall, make sure you have activated the environment
$ conda activate TEsmall
For example, you would like to apply TEsmall on 2 FASTQ files:
$ TEsmall -f Parental_1.fastq.gz DroKO_1.fastq.gz -l Parental DroKO
When it's done, deactivate the environment
$ conda deactivate
If you would like to specify the directory to which the genomes TEsmall uses for annotation are downloaded and read from, you can specify it at runtime using the
$ TEsmall -f Parental_1.fastq.gz DroKO_1.fastq.gz -g hg19 -l Parental DroKO --dbfolder /path/to/another/folder/
The files used by TEsmall will be downloaded to/access from the
The default location is
For more information
$ TEsmall -h usage: TEsmall [-h] [-a STR] [-m INT] [-M INT] [-g STR] [--maxaln INT] [--mismatch INT] [-o STR [STR ...]] [-p INT] [-f STR [STR ...]] [-l STR [STR ...]] [--dbfolder STR] [--verbose INT] [-v] optional arguments: -h, --help show this help message and exit -a STR, --adapter STR Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. (default: TGGAATTCTCGGGTGCCAAGG) -m INT, --minlen INT Discard trimmed reads that are shorter than INT. Reads that are too short even before adapter removal are also discarded. (default: 16) -M INT, --maxlen INT Discard trimmed reads that are longer than INT. Reads that are too long even before adapter removal are also discarded. (default: 36) -g STR, --genome STR Version of reference genome (hg19, mm9, or dm3; default: hg19) --maxaln INT Suppress all alignments for a particular read if more than INT reportable alignments exist for it. (default: 100) --mismatch INT Report alignments with at most INT mismatches. (default: 0) -o STR [STR ...], --order STR [STR ...] Annotation priority. (default: structural_RNA miRNA hairpin exon TE intron piRNA_cluster) -p INT, --parallel INT Parallel execute by INT CPUs. (default: 1) -f STR [STR ...], --fastq STR [STR ...] Input in FASTQ format. Compressed input is supported and auto-detected from the filename extension (.gz). -l STR [STR ...], --label STR [STR ...] Unique label for each sample. --dbfolder STR Custom location of TEsmall database folder (containing the "genomes" folder). DEFAULT: $HOME/TEsmall_db/ --verbose INT Set verbose level. 0: only show critical message 1: show additional warning message 2: show process information 3: show debug messages. DEFAULT: 2 -v, --version show program's version number and exit
Copying & distribution
TEsmall is part of TEToolkit suite.
TEsmall is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with TEsmall. If not, see this website.
If using the software in a publication, please cite the following:
O'Neill K, Liao WW, Patel A, Hammell MG. (2018) TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Front Genet. Oct 5;9:461.