CellRanger-TE is a modification to the Cell Ranger reference database that enables the software to quantify transposable elements from single-cell and single-nuclei datasets.
It takes the GENCODE FASTA and gene annotations, filters them according to the instructions provided by 10x Genomics regarding reference databases, and adds the TE annotations to create a TE-aware reference database
This is currently only available for mouse (GRCm39) and human (GRCh38).
Website: Molly Gale Hammell Lab
Contact: mghcompbio@gmail.com
sh CellRanger-TE_database_generation.sh -g [genome build] -r [release version]
genome build: GRCh38 or GRCm39
default release version is 35 (human) and M26 (mouse)Please note that GENCODE release 20 (human) and M26 (mouse) are the oldest releases corresponding to GRCh38 and GRCm39 respectively. Specifying older GENCODE releases will throw an error.
We recommend providing 10 CPU/cores and 250Gb of memory to ensure successful completion of the script.
CellRangerTE is free softrware: 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 TEtranscripts. If not, see this website.
Available soon...