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--- myillu_01.trimpe.sh [2016/05/07 12:52] – hyjeong
+++ myillu_01.trimpe.sh [2021/03/17 13:09] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Script myIllu_trimPE.sh ======
+====== Script <myIllu_trimPE.sh> ======
   #!/bin/bash
@@ Line 6: / Line 6: @@
   # Trimmomatic v0.32 manual:
   #   http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
+  #
+  # Latest version of ngopt (a5_miseq): 20150522
   TRIMMOMATIC=/usr/local/apps/a5_miseq_linux_20140604/bin/trimmomatic.jar
@@ Line 12: / Line 14: @@
   THREADS=24
   MINLEN=75
+  # default MINLENG is 75 (for NGOPT, 36 bp)
   if [ $# -ne 2 ]
@@ Line 27: / Line 30: @@
   done
+  # Using `basename` command is a good idea. Because the stripped BASE
+  # can be used as a output file prefix in "current" directory.
   BASE=$(basename "$1")  # delete any leading path
   BASE=${BASE%_*}           # delete string from '_' to the end (shortest match)
-  # BASE=${1%%_*} makes difference. What is it?
+  # BASE=${1%%_*} makes difference. What is it? (longest match)
-  # BASE=${1/_*/}
+  # BASE=${1/_*/} (longest match)
   echo "File name base: $BASE"
+  BASE=${BASE}-trim
+  echo "File name base will be changed into ${BASE}"
   java -jar $TRIMMOMATIC PE -threads ${THREADS} -phred33 -baseout ${BASE}.fq.gz $1 $2 ILLUMINACLIP:$ADAPTER:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:${MINLEN}