Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ElementoLab/scTCRseq
Processing of single cell RNAseq data for the recovery of TCRs in python
https://github.com/ElementoLab/scTCRseq
python rna-seq single-cell-rna-seq
Last synced: 23 days ago
JSON representation
Processing of single cell RNAseq data for the recovery of TCRs in python
- Host: GitHub
- URL: https://github.com/ElementoLab/scTCRseq
- Owner: ElementoLab
- License: agpl-3.0
- Created: 2016-05-11T14:49:26.000Z (about 8 years ago)
- Default Branch: main
- Last Pushed: 2020-11-25T16:43:06.000Z (over 3 years ago)
- Last Synced: 2024-02-24T15:32:57.495Z (4 months ago)
- Topics: python, rna-seq, single-cell-rna-seq
- Language: Python
- Size: 23.4 KB
- Stars: 25
- Watchers: 15
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Lists
- awesome_single_cell - scTCRseq - [python] - Map T-cell receptor (TCR) repertoires from single cell RNAseq. (Software packages / RNA-seq)
- awesome-single-cell - scTCRseq - [python] - Map T-cell receptor (TCR) repertoires from single cell RNAseq. (Software packages / RNA-seq)
- awesome-single-cell - scTCRseq - [python] - Map T-cell receptor (TCR) repertoires from single cell RNAseq. (Software packages / RNA-seq)
README
# scTCRseq
## IntroductionFor specific questions/problems please email David Redmond at: [email protected]
This project is an implementation of a pipeline for Single-cell RNAseq package for recovering TCR data in python
[Github Project](https://github.com/ElementoLab/scTCRseq)
## Configuration and Dependencies
The pipeline needs for the following programs to be installed and the paths :###SEQTK:
https://github.com/lh3/seqtk###Blastall:
http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast/executables/release/2.2.15/###GapFiller:
http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller###Vidjil:
https://github.com/vidjil/vidjilAnd their accompanying paths need to be changed in the script cmd_line_sctcrseq.py:
seqTkDir="/path/to/seqtk/"
blastallDir="/path/to/blastall/"
gapFillerDir="/path/to/GapFiller_v1-10_linux-x86_64/"
vidjildir="/path/to/vidjil/"
lengthScript="/path/to/calc.median.read.length.pl"
###Reference TCR sequences:
Also the user can select their chosen TCR alpha and beta V and C reference databases (we recommend downloading from imgt.org) and enter their locations:
location for FASTA BLAST reference sequences downloadable from imgt.org - (needs to be changed manually)
humanTRAVblast="/path/to/TRAV.human.fa"
humanTRBVblast="/path/to/TRBV.human.fa"
humanTRACblast="/path/to/TRAC.human.fa"
humanTRBCblast="/path/to/TRBC.human.fa"
mouseTRAVblast="/path/to/TRAV.mouse.fa"
mouseTRBVblast="/path/to/TRBV.mouse.fa"
mouseTRACblast="/path/to/TRAC.mouse.fa"
mouseTRBCblast="/path/to/TRBC.mouse.fa"
location for Vidjil BLAST reference sequences in vidjil program - (needs to be changed manually)
humanVidjilRef="/path/to/tr_germline/human"
mouseVidjilRef="/path/to/tr_germline/mouse"
## Example Command Line
We recommend running the pipeline on paired end fluidigm single cell RNA seq data.
The usage is as follows:
####python cmd_line_sctcrseq.py --fastq1 FASTQ1 --fastq2 FASTQ2 --species human/mouse --outdir OUTPUT DIRECTORY --label OUTPUT LABEL
Also running:
####python cmd_line_sctcrseq.py
Will give command line options
To test the program we recommend either using your own single cell RNA sequencing data or downloading data such as at
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1104129