#!/bin/bash
#
# Script used for paired end trimming of MII H3K36me3 and 2-cell H3K9me3 ChIP-seq
# In case of questions contact Mads Lerdrup - mads.lerdrup@sund.ku.dk

BASE_DIR=/isilonsund/NextGenSeqData/project-data/lerdrup/temp/adeel/am47_AMASN-139703566
TRIM_DIR=${BASE_DIR}/trimmed
ADAPTER_FASTA_FILE=/k/genomes/adapters/fa/adapters.fa
TM_PATH=/home/lerdrup/programs/Trimmomatic-0.39/trimmomatic-0.39.jar

mkdir -p ${TRIM_DIR}
cd ${TRIM_DIR}

for f in `ls ${BASE_DIR}/*_R1.fastq.gz`;do
  FQ=${BASE_DIR}/`basename $f _R1.fastq.gz`
  TRIMOUT=${TRIM_DIR}/`basename $f _R1.fastq.gz`

  echo "nice java -Xmx5g -jar ${TM_PATH} PE ${FQ}_R1.fastq.gz ${FQ}_R2.fastq.gz ${TRIMOUT}_trim_R1P.fastq.gz ${TRIMOUT}_trim_R1U.fastq.gz ${TRIMOUT}_trim_R2P.fastq.gz ${TRIMOUT}_trim_R2U.fastq.gz ILLUMINACLIP:${ADAPTER_FASTA_FILE}:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:5 CROP:125 MINLEN:30 > ${TRIMOUT}_trimmomatic.log 2>&1"
  echo

done | parallel -j 8

# Used earlier by Rehanna for PE75 reads: ILLUMINACLIP:/data/rqd281/PROGRAMS/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:5 CROP:50 MINLEN:30