Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

CITE-seq-Count is a python package that counts antibody TAGS. It handles the data from both the Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seqi) and/or Cell Hashing experiment.

References:

• Eleni Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengquing Ouyang, Rahul Satija, Neville E. Sanjana, Sergei B Koralov, Peter Smibert
  Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
  bioRxiv preprint doi: https://doi.org/10.1101/466466.

• CITE-seq-Count Github page
• CITE-seq-Count manual

• Module Name: CITE-seq-Count (see the modules page for more information)
• Unusual environment variables set
  • CSCOUNT_HOME  installation directory
  • CSCOUNT_BIN  executable directory
  • CSCOUNT_SRC  source code directory
  • CSCOUNT_TESTS  test scripts directory
  • CSCOUNT_DATA   sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3104 ~]$ module load citeseqcount/1.4.3
[+] Loading citeseqcount 1.4.3  ...

Copy the testing scripts and data to your current folder and run the scripts:

[user@cn3104 ~]$ cp $CSCOUNT_TESTS/*.py .
[user@cn3104 ~]$ cp -r $CSCOUNT_DATA . 
[user@cn3104 ~]$ python test_io.py 
[user@cn3104 ~]$ python test_preprocessing.py    
[user@cn3104 ~]$ python test_processing.py  

Exit the application:

[user@cn3104 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$