Newer
Older
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
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
#!/bin/bash
#SBATCH --job-name=star_index
#SBATCH --partition=super
#SBATCH --nodes=1
#SBATCH --time=0-24:00:00
#SBATCH --output=star_index.%j.out
#SBATCH --error=star_index.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
module load iGenomes/2013-03-25
module load star/2.4.2a
STAR --runMode genomeGenerate --genomeFastaFiles $iGENOMES_DB_DIR\/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa --sjdbOverhang 100 --sjdbGTFfile /project/GCRB/shared/Gencode_human/release_19/gencode.v19.annotation.gtf --runThreadN 8 --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0 --outFileNamePrefix gencode.v19.annotation
#!/bin/bash
#SBATCH --job-name=rsem_index
#SBATCH --partition=super
#SBATCH --nodes=1
#SBATCH --time=0-24:00:00
#SBATCH --output=rsem_index.%j.out
#SBATCH --error=rsem_index.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
module load iGenomes/2013-03-25
module load RSEM/1.2.31
rsem-prepare-reference --gtf /project/GCRB/shared/Gencode_human/release_19/gencode.v19.annotation.gtf $iGENOMES_DB_DIR\/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0
#!/bin/bash
#SBATCH --job-name=star_align
#SBATCH --partition=super
#SBATCH --nodes=1
#SBATCH --time=0-24:00:00
#SBATCH --output=star_align.%j.out
#SBATCH --error=star_align.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
module load iGenomes/2013-03-25
module load star/2.4.2a
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/ERR266338.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/align-star.sh-1.0.0/ERR266338
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/ERR266344.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/align-star.sh-1.0.0/ERR266344
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/ERR266349.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/align-star.sh-1.0.0/ERR266349
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/ERR266333.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/align-star.sh-1.0.0/ERR266333
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/ERR266335.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/align-star.sh-1.0.0/ERR266335
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/ERR266342.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/align-star.sh-1.0.0/ERR266342
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/ERR266351.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/align-star.sh-1.0.0/ERR266351
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/ERR266346.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/align-star.sh-1.0.0/ERR266346
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/ERR266341.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/align-star.sh-1.0.0/ERR266341
STAR --genomeDir /project/GCRB/shared/Gencode_human/release_19/prep-star.sh-1.0.0/ --readFilesIn /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/ERR266337.fastq.gz \
--readFilesCommand zcat --genomeLoad NoSharedMemory \
--outFilterMultimapNmax 1000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate \
--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
--outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/align-star.sh-1.0.0/ERR266337
#!/bin/bash
#SBATCH --job-name=rsem_quant
#SBATCH --partition=super
#SBATCH --nodes=1
#SBATCH --time=0-24:00:00
#SBATCH --output=rsem_quant.%j.out
#SBATCH --error=rsem_quant.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
module load RSEM/1.2.31
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/align-star.sh-1.0.0/ERR266344Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/quant-rsem.sh-1.0.0/ERR266344Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/align-star.sh-1.0.0/ERR266338Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D10/quant-rsem.sh-1.0.0/ERR266338Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/align-star.sh-1.0.0/ERR266349Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/quant-rsem.sh-1.0.0/ERR266349Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/align-star.sh-1.0.0/ERR266333Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D2/quant-rsem.sh-1.0.0/ERR266333Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/align-star.sh-1.0.0/ERR266335Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/quant-rsem.sh-1.0.0/ERR266335Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/align-star.sh-1.0.0/ERR266342Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D0/quant-rsem.sh-1.0.0/ERR266342Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/align-star.sh-1.0.0/ERR266346Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/quant-rsem.sh-1.0.0/ERR266346Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/align-star.sh-1.0.0/ERR266351Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D7/quant-rsem.sh-1.0.0/ERR266351Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/align-star.sh-1.0.0/ERR266337Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/quant-rsem.sh-1.0.0/ERR266337Aligned_rsem
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/align-star.sh-1.0.0/ERR266341Aligned.toTranscriptome.out.bam /project/GCRB/shared/Gencode_human/release_19/prep-rsem.sh-1.0.0/gencode.v19.annotation /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/RNA-seq/ES_D5/quant-rsem.sh-1.0.0/ERR266341Aligned_rsem