rnaseq_analysis_on_allfiles.lsf

#!/bin/bash
#
#BSUB -q priority       # Partition to submit to (comma separated)
#BSUB -n 6                  # Number of cores
#BSUB -W 1:30               # Runtime in D-HH:MM (or use minutes)
#BSUB -R "rusage[mem=4000]"    # Memory in MB
#BSUB -J rnaseq_mov10         # Job name
#BSUB -o %J.out       # File to which standard out will be written
#BSUB -e %J.err       # File to which standard err will be written


for fq in ~/unix_workshop/rnaseq_project/data/trimmed_fastq/*.fq
do
  sh ~/unix_workshop/rnaseq_project/rnaseq_analysis_on_input_file.sh $fq
done

countmatrix=results/counts/Mov10_rnaseq_counts.txt

# Concatenate all count files into a single count matrix
paste results/counts/Mov10_oe_1.counts results/counts/Mov10_oe_2.counts results/counts/Mov10_oe_3.counts results/counts/Irrel_kd_1.counts results/counts/Irrel_kd_2.counts results/counts/Irrel_kd_3.counts | awk '{print$1"\t"$2"\t"$4"\t"$6"\t"$8"\t"$10"\t"$12}' | grep -v "^__" > $countmatrix