Mercurial > repos > mingchen0919 > gtg_star_demo

view run-star-jobs.sh @ 1:44632fc0fc15 draft

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update
author mingchen0919
date Wed, 20 Jun 2018 11:33:55 -0400
parents a1448d1f2ee4
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cd ${REPORT_FILES_PATH}
mkdir -p scripts

# index genome
grep -v None ${TOOL_INSTALL_DIR}/1-index-genome.sh > scripts/1-index-genome.sh
sh scripts/1-index-genome.sh

# mapping
grep -v None ${TOOL_INSTALL_DIR}/2-mapping.sh > scripts/2-mapping.sh
sh scripts/2-mapping.sh

# convert sam to bam
cp ${TOOL_INSTALL_DIR}/3-sam2bam.sh scripts/3-sam2bam.sh
sh scripts/3-sam2bam.sh

# mapping evaluation
cp ${TOOL_INSTALL_DIR}/4-flagstat.sh scripts/4-flagstat.sh
sh scripts/4-flagstat.sh