htseq_count.sh 3.25 KB
Newer Older
Venkat Malladi's avatar
Venkat Malladi committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
#!/bin/bash

#SBATCH --job-name=ddx21_counts
#SBATCH --partition=super
#SBATCH --nodes=1
#SBATCH --time=0-24:00:00
#SBATCH --output=ddx21_counts.%j.out
#SBATCH --error=ddx21_counts.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL

## Load the prerequisite modules
module load HTSeq/0.6.1


ANOTATION='/project/GCRB/shared/Gencode_human/release_19_ERCC_92/merge-annotation.sh-1.1.0/gencode.v19.annotation_ERCC_92.gtf'

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/LucKD/spike/align-tophat-se.sh-1.0.0/LucKD-1_S1_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/LucKD-1.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/LucKD/spike/align-tophat-se.sh-1.0.0/LucKD-2_S5_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/LucKD-2.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD_pos_Mut_DDX21/spike/align-tophat-se.sh-1.0.0/DDX21_1KD_pos_Mut_DDX21-1_S4_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_Mut_DDX21-1.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD_pos_Mut_DDX21/spike/align-tophat-se.sh-1.0.0/DDX21_1KD_pos_Mut_DDX21_S8_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_Mut_DDX21-2.counts


htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD/spike/align-tophat-se.sh-1.0.0/DDX21_1KD-2_S6_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD-2.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD/spike/align-tophat-se.sh-1.0.0/DDX21_1KD-1_S2_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD-1.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD_pos_WT_DDX21/spike/align-tophat-se.sh-1.0.0/DDX21_1KD_pos_WT_DDX21-2_S7_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_WT_DDX21-2.counts

htseq-count \
-f bam \
-m intersection-nonempty \
-i gene_id \
-r pos \
-s no \
/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/DDX21_1KD_pos_WT_DDX21/spike/align-tophat-se.sh-1.0.0/DDX21_1KD_pos_WT_DDX21-1_S3_R1_001.fastq.gz.accepted_hits.bam $ANOTATION > /project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_WT_DDX21-1.counts