Repeat pseudo-genome preparation

To map reads to repetitive elements, we created a pseudo-genome that only contains the repeat sequences. The used in house scripts are available here. In summary the pseudo-genome can be created as follows (in a Linux operating system)

Required software:

Make sure the following software are installed and:

• python version 2.7.3

• bowtie 1 version 0.12.9

• bedtools version 2.20.1

• samtools version >=1.6

• Picard tools >= 2.6.0

• STAR >=2.5.2b 

Make sure that the Biopython library is installed

pip install BioPython

Download required files:

1. Clone our code repository

   git clone https://github.com/sirusb/2CLike_analysis.git

2. Go to the Pseudogenome folder

   cd Pseudogenome

3. Download the mm9 repeats annotation from RepEnrich google-dive here and put in the Pseudogenome folder.

4. Decompress the downloaded 'mm9_repeatmasker_clean.txt.gz` file as follows:

   gunzip mm9_repeatmasker_clean.txt.gz

5. Create an mm9 fasta file that contains all the chromosomes present in the 'mm9_repeatmasker_clean.txt.gz` using the following bash script:

   chroms=`cat mm9_repeatmasker_clean.txt  | awk '{print $5}' | uniq  | grep chr` 

   genome_version='mm9' 

   ## Download the different chromosome .fa files 

   for f in $chroms 

   do      

    echo "Downloading chr${f}.fa.gz"      

    wget http://hgdownload.cse.ucsc.edu/goldenPath/${genome_version}/chromosomes/${f}.fa.gz -O ${f}.fa.gz     zcat ${f}.fa >> ${genome_version}.fa 

   done 

   ## Remove intermediate files 

   echo "removing intermediate files" 

   rm chr*.fa.gz

   
   

6. Open the file run_buildPseudogenome.sh and edit the path to Picard tools.

7. Run the run_buildPseudogenome.sh script

   sh run_buildPseudogenome.sh

8. Once the script finish running it will create the rms_Pseudo_out folder that contains the newly created genome and its STAR index.
   

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