#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N dropseq_10X_P4_2_New_UseThis_omp28
#$ -pe omp 28
#$ -l mem_per_core=18G
#$ -l h_rt=72:00:00
echo "=========================================================="
echo "Starting on       : $(date)"
echo "Running on node   : $(hostname)"
echo "Current job ID    : $JOB_ID"
echo "Current job name  : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="

source ~/.bashrc

module load bcl2fastq/2.20
module load cellranger/2.1.1


cellranger count --id="10X_P4_2_New_UseThis" --transcriptome="/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups"  --fastqs="/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/library/10X_P4_2/10X_P4_2_MissingLibrary_1_H2HT7DMXX" --sample="bamtofastq"  --expect-cells=3000

echo "Finished  .............. $(date)"