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1 #!/bin/bash
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2
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3 if [ "$#" -ne 1 ]; then
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4 echo "[usage:] expression.sh bam.file"
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5 exit 1;
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6 fi
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7
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8 INPUT_BAM=$1
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9 SAMPLE_ID="sample"
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10 SAMTOOLS=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/samtools
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11 HTSEQ_COUNT=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/htseq-count
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12 GTF=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/gencode.v22.annotation.gtf
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13 EXPRESSION_R=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/expression.r
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14
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15 HTSEQ_COUNT_OUT=./$SAMPLE_ID".htseq-count.out"
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16 EXPRESSION_OUT=./out
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17 EXPRESSION_OUT_TMP=./out_tmp
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18
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19 rm -rf $EXPRESSION_OUT
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20 rm -rf $EXPRESSION_OUT_TMP
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21
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22 mkdir $EXPRESSION_OUT
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23 mkdir $EXPRESSION_OUT_TMP
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24
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25
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26 $SAMTOOLS view -F 4 $INPUT_BAM |
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27 $HTSEQ_COUNT \
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28 -m intersection-nonempty \
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29 -i gene_id \
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30 -r pos \
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31 -s no \
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32 - $GTF > $HTSEQ_COUNT_OUT
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33
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34 Rscript $EXPRESSION_R $HTSEQ_COUNT_OUT
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35
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36 mv $EXPRESSION_OUT_TMP/$SAMPLE_ID".txt" $EXPRESSION_OUT/
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37
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