firt script

Trim_and_compare.sh

+#!/bin/bash
+################################################################################
+#                              TrimAndCompare                                  #
+#                                                                              #
+# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. Place a short           #
+# description of the script here.                                              #
+#                                                                              #
+#  Copyright (C) 2020 Rahma Amen (Potsdam University)                          #
+#  LinuxGeek46@both.org                                                        #
+#                                                                              #
+# Change History                                                               #
+#   16/07/2020  Rahma Amen  created the script (inspired from Johanna Krger)  #
+#                                                                              #
+#                                                                              #
+################################################################################
+
+######
+### Trimming
+######
+
+ODIR=/home/mohamed/work/RAHMA/Analysis/
+IDIR=/home/mohamed/work/RAHMA/RUN/
+fqcdir=/home/mohamed/work/RAHMA/fastqc_analysis/
+#ODIR=/home/bsdb2425/Rahma/temp/trimmed_capture-v1/
+#IDIR=/home/bsdb2425/Rahma/temp/
+ADAPTER_FWD=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+ADAPTER_REV=TTACTATGCCGCTGGTGGCTCTAGATGTGNNNNNNNTGTGAGAAAGGGATGTGCTGCGAGAAGG
+TSeqfile=/home/mohamed/work/RAHMA/fastqc_analysis/TotalSeq_report
+
+mkdir -p $ODIR
+mkdir -p $fqcdir
+
+#for file in `ls $INDIR/*R1*.fastq`
+for fastqf in $IDIR/*R1_001.fastq.gz
+
+do
+    # file stem (without extension or path)
+    fstem=$(echo $fastqf | sed 's/.*\///' | sed 's/1_001.fastq.gz//')
+    # fastq file names (original and trimmed)
+    f1o=$IDIR$fstem"1_001.fastq.gz"
+    f1t=$ODIR$fstem"1_001_trimmed.fastq.gz"
+    f2o=$IDIR$fstem"2_001.fastq.gz"
+    f2t=$ODIR$fstem"2_001_trimmed.fastq.gz"
+
+    cutadapt -a $ADAPTER_FWD -A $ADAPTER_REV -q 20 -m 30 -o $f1t -p  $f2t $f1o $f2o 
+
+    # fastqc for all files
+    fastqc --extract --outdir=$fqcdir $f1o $f2o $f1t $f2t 
+#    fastqc --extract --outdir=$fqcdir $f1o $f1t
+
+    # remove zip files
+    rm $fqcdir/$fstem*.zip
+
+    f1oqc=$fqcdir$fstem"1_001_fastqc/fastqc_data.txt"
+    TotalSeq1o=`grep "Total Seq" $f1oqc | sed 's/Total Sequences	//' `
+    echo $TotalSeq1o
+    f1tqc=$fqcdir$fstem"1_001_trimmed_fastqc/fastqc_data.txt"
+    TotalSeq1t=`grep "Total Seq" $f1tqc | sed 's/Total Sequences	//' `
+    echo $TotalSeq1t
+
+    f2oqc=$fqcdir$fstem"2_001_fastqc/fastqc_data.txt"
+    TotalSeq2o=`grep "Total Seq" $f2oqc | sed 's/Total Sequences	//' `
+    f2tqc=$fqcdir$fstem"2_001_trimmed_fastqc/fastqc_data.txt"
+    TotalSeq2t=`grep "Total Seq" $f2tqc | sed 's/Total Sequences	//' `
+    
+    echo "${fstem}1_001: $TotalSeq1o   $TotalSeq1t" >   $TSeqfile
+    echo "${fstem}2_001: $TotalSeq2o   $TotalSeq2t" >>  $TSeqfile
+
+done
+
+