# Author: Rehannah Borup Helweg-Larsen
# Script for trimming and alignment of MII H3K4me3 ChIP-seq and MII H3K9me3 ChIP-seq samples 

##### Processing of MII H3K4me3 ChIP-seq - Paired End samples
# trim fastq files with Trimmomatic-0.36
java -jar trimmomatic-0.36.jar PE -threads 10 -phred33  $input_R1.fastq.gz $input_R2.fastq.gz /
 $output_paired_1.fastq.gz $output_unpaired_1.fastq.gz $output_paired_2.fastq.gz $output_unpaired_2.fastq.gz /
 ILLUMINACLIP:/data/rqd281/PROGRAMS/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:15 CROP:120 MINLEN:40

# mapping of paired trimmed fastq with bowtie2 to reference GFT: Gencode Mouse v.16 (GRCm38)

 while read sample; do
  R1=$output_paired_1.fastq.gz
  R2=$output_paired_2.fastq.gz
  bowtie2 --local -X 2000 -x  ./bowtie_index/vm16.GRCm38.bowtie -1 $R1 -2 $R2 -S $output.sam -p 11
 done < fastq.sample.list


#### Prossesing of MII H3K9me3 ChIP-seq  - Paired End samples

# trim fastq files with Trimmomatic-0.36
java -jar trimmomatic-0.36.jar  PE -threads 10 -phred33  $input_fastq.R1 $input_fastq.R2 /
 $output_paired_1.fastq.gz $output_unpaired_1.fastq.gz $output_paired_2.fastq.gz $output_unpaired_2.fastq.gz /
 ILLUMINACLIP:Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:5 CROP:50 MINLEN:30

# mapping with bowtie2 to reference GFT: Gencode Mouse v.16 (GRCm38)
  R1=$output_paired_1.fastq.gz
  R2=$output_paired_2.fastq.gz
  bowtie2 --local -X 2000 -x  ./bowtie_index/vm16.GRCm38.bowtie -1 $R1 -2 $R2 -S $output.sam -p 11