#!/bin/bash -l
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N mm10Annot_ensembl_GeneBody_TACOTishaEnsmblNRLincs
#$ -pe omp 8
#$ -l mem_per_core=2G
#$ -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
#old version used to run tabula muris data
#module load bcl2fastq/2.20
#module load cellranger/2.1.1
module load python2
module load bcl2fastq/2.20
module load cellranger/3.1.0


######### This is for PCG+48K annotated lncs+ 7 gene of interest################################
#cellranger mkref --genome="mm10Annot_premrna_PCG-newlncs_GeneBody_TACOTisha" --fasta="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/genome.fa" --genes="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/Final_48KTACOTisha_7GOI_Genebody_mm10Annot.gtf"

######### This is for PCG+48K annotated lncs+ 7 gene of interest+ 4796Ensmbl lincs and antisense  ################################
cellranger mkref --genome="mm10Annot_premrna_PCG-newlncs_GeneBody_TACOTishaEnsmblNRLincs" --fasta="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/genome.fa" --genes="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/Final_48KTACOTisha_7GOI_EnsmblLincAntisense_Genebody_mm10Annot.gtf"


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