Mercurial > repos > mingchen0919 > aurora_htseq

view run_htseq-count.sh @ 6:7c54fd452b8e draft

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add kableExtra package
author mingchen0919
date Wed, 18 Apr 2018 15:59:38 -0400
parents aacd5f53ac99
children
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cd ${X_d}

cat >htseq-count.sh <<EOF
  htseq-count \\
    $(echo ${X_A} | sed 's/,/ /g') \\
    ${X_G} \\
    -f ${X_f} \\
    -r ${X_r} \\
    -s ${X_S} \\
    -a ${X_a} \\
    -t ${X_T} \\
    -i ${X_i} \\
    -m ${X_m} > htseq-counts-raw.txt 
    
  grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
  
  cp counts.txt ${X_c}
EOF

sh htseq-count.sh