For 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
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/vidjil
And 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"
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