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custom_scripts_for_16s_rrna_sequence_analysis

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custom_scripts_for_16s_rrna_sequence_analysis [2019/09/09 21:51]
hyjeong created
custom_scripts_for_16s_rrna_sequence_analysis [2019/09/09 21:51] (current)
hyjeong [merge_paired_fastq.sh]
Line 7: Line 7:
   # https://​github.com/​edamame-course/​Amplicon_Analysis/​blob/​master/​resources/​Merged_Reads_Script.sh   # https://​github.com/​edamame-course/​Amplicon_Analysis/​blob/​master/​resources/​Merged_Reads_Script.sh
   #   #
 +  ​
   out=merged_dir   out=merged_dir
 +  ​
   if [ ! -d merged_reads ]; then   if [ ! -d merged_reads ]; then
       echo Creating ${out} directory...       echo Creating ${out} directory...
       mkdir ${out}       mkdir ${out}
   fi   fi
 +  ​
   for f in *F_sub.*   for f in *F_sub.*
   do   do
 +  ​
       if [ ! -e ${f} ]; then       if [ ! -e ${f} ]; then
           echo Can\'t find '​F_sub'​ reads!           echo Can\'t find '​F_sub'​ reads!
Line 23: Line 23:
           exit           exit
       fi       fi
 +  ​
       r=$(sed -e "​s/​F_sub/​R_sub/"​ <<<​ "​$f"​)       r=$(sed -e "​s/​F_sub/​R_sub/"​ <<<​ "​$f"​)
       file=$(cut -d_ -f1 <<<​ "​$f"​)       file=$(cut -d_ -f1 <<<​ "​$f"​)
custom_scripts_for_16s_rrna_sequence_analysis.txt ยท Last modified: 2019/09/09 21:51 by hyjeong