Commit 7afd0e0b authored by Hasan Celik's avatar Hasan Celik
Browse files

.sh script deleted

parent 504ad38f
Pipeline #2191 failed with stages
in 3 seconds
GENOMEDIR='/s/genomes/droMel/r6.22/star-indexes'
DATAPATH='/s/project/gagneurlab_shared/chipseq-polycomb/analysis-november-2018/'
NUMTHEADS=48
CHIPSEQFILESFIRSTPAIR=(
# 'Input_esc_0-6hr_S3_R1_001'
# 'Input_WT_0-6hr.conc.R1'
# 'Input_WT_18-24hr_S7_R1_001'
# 'H3K27me3_ChIP_esc_0-6hr_S4_R1_001'
# 'H3K27me3_ChIP_WT_0-6hr.conc.R1'
# 'H3K27me3_ChIP_WT_18-24hr_S5_R1_001'
# 'Input_esc_18-24hr.conc.R1'
# 'Input_WT_0-6hr_S2_R1_001'
# 'H3K27me3_ChIP_esc_18-24hr.conc.R1'
# 'H3K27me3_ChIP_WT_0-6hr_S1_R1_001'
# 'Input_esc_0-6hr.conc.R1'
'Input_esc_18-24hr_S6_R1_001'
'Input_WT_18-24hr.conc.R1'
'H3K27me3_ChIP_esc_0-6hr.conc.R1'
'H3K27me3_ChIP_esc_18-24hr_S8_R1_001'
'H3K27me3_ChIP_WT_18-24hr.conc.R1'
)
CHIPSEQFILESSECONDPAIR=(
# 'Input_esc_0-6hr_S3_R2_001'
# 'Input_WT_0-6hr.conc.R2'
# 'Input_WT_18-24hr_S7_R2_001'
# 'H3K27me3_ChIP_esc_0-6hr_S4_R2_001'
# 'H3K27me3_ChIP_WT_0-6hr.conc.R2'
# 'H3K27me3_ChIP_WT_18-24hr_S5_R2_001'
# 'Input_esc_18-24hr.conc.R2'
# 'Input_WT_0-6hr_S2_R2_001'
# 'H3K27me3_ChIP_esc_18-24hr.conc.R2'
# 'H3K27me3_ChIP_WT_0-6hr_S1_R2_001'
# 'Input_esc_0-6hr.conc.R2'
'Input_esc_18-24hr_S6_R2_001'
'Input_WT_18-24hr.conc.R2'
'H3K27me3_ChIP_esc_0-6hr.conc.R2'
'H3K27me3_ChIP_esc_18-24hr_S8_R2_001'
'H3K27me3_ChIP_WT_18-24hr.conc.R2'
)
CHIPSEQFILESFINAL=(
# 'Input_esc_0-6hr_S3_001'
# 'Input_WT_0-6hr.conc'
# 'Input_WT_18-24hr_S7_001'
# 'H3K27me3_ChIP_esc_0-6hr_S4_001'
# 'H3K27me3_ChIP_WT_0-6hr.conc'
# 'H3K27me3_ChIP_WT_18-24hr_S5_001'
# 'Input_esc_18-24hr.conc'
# 'Input_WT_0-6hr_S2_001'
# 'H3K27me3_ChIP_esc_18-24hr.conc'
# 'H3K27me3_ChIP_WT_0-6hr_S1_001'
# 'Input_esc_0-6hr.conc'
'Input_esc_18-24hr_S6_001'
'Input_WT_18-24hr.conc'
'H3K27me3_ChIP_esc_0-6hr.conc'
'H3K27me3_ChIP_esc_18-24hr_S8_001'
'H3K27me3_ChIP_WT_18-24hr.conc'
)
for ((i=0;i<${#CHIPSEQFILESFIRSTPAIR[@]};++i));
do
CHIPSEQFILE=${CHIPSEQFILESFINAL[i]}
CHIPSEQFP=$DATAPATH${CHIPSEQFILESFIRSTPAIR[i]}'.fastq.gz'
CHIPSEQSP=$DATAPATH${CHIPSEQFILESSECONDPAIR[i]}'.fastq.gz'
CHIPSEQBAM=$CHIPSEQFILE'.bam'
echo $CHIPSEQFILE
STAR --runMode alignReads --genomeDir $GENOMEDIR --readFilesIn $CHIPSEQFP $CHIPSEQSP --readFilesCommand zcat --alignIntronMax 1 --seedSearchStartLmax 30 --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --runThreadN $NUMTHEADS
samtools view -hb -q 255 -@ $NUMTHEADS Aligned.out.sam | samtools sort -m 32G -@ $NUMTHEADS -o $CHIPSEQBAM -
samtools index $CHIPSEQBAM
mkdir $CHIPSEQFILE
mv ./*.out $CHIPSEQFILE
mv ./*.tab $CHIPSEQFILE
mv ./*.sam $CHIPSEQFILE
mv ./*.bam $CHIPSEQFILE
mv ./*.bam.bai $CHIPSEQFILE
done
GENOMEDIR='/s/genomes/droMel/r6.22/star-indexes'
GENOMEPATH='/s/genomes/droMel/r6.22/dmel-all-chromosome-r6.22.fasta'
GTFPATH='/s/genomes/droMel/r6.22/dmel-all-r6.22.gtf'
NUMTHEADS=48
STAR \
--runMode genomeGenerate \
--genomeDir $GENOMEDIR \
--genomeFastaFiles $GENOMEPATH \
--sjdbGTFfile $GTFPATH \
--runThreadN $NUMTHEADS
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