ME-Scan analysis codes for the Alu, LINE, and SVA libraries.

MEScanner is an intergrated tool for identifying polymorphic mobile element insertions (MEIs) using targeted high throughput sequencing.

• Author: Hongseok Ha, JuiWan Loh, Jinchuan Xing
• Current version : 1.2
• Last update date : 10 April 2016
• Homepage: http://xinglab.genetics.rutgers.edu/
• Programmer's contact: hha@hotmail.com
• PI's contact: xing@biology.rutgers.edu

Requirements: BWA, Blast, LiftOver, Samtools, Bedtools, Primer3

To run the code:

1. Download whole code and source the main command source software_path/ME-SCAN.sh.
2. Download and modify reference files based on the README in each "ref_*" subdirectories.
3. Creat a pathfile named as "ME-Scan.path" and a parameter file with ".parameters" as the extension in the working directory.
4. The working directory should include subdirectories named as "Sample_...*" that contain Fastq files in pair-end format.
5. Running the main command ME-SCAN.sh.

Folders:

• family_info: pedigree files for all samples used in the study
• parameters_info: parameters files used in the study
• modules: individual analysis modules
• ref_blast
• ref_encode
• ref_gencode
• ref_mescan

The .parameters file includes the following parameters:

<parameter>

• MEI_ref_RM ==> Name of the MEI to be used in the reference genome RepeatMasker annotation
• MEI_known_stewart ==> Name of the pMEIs to be extracted from Stewart et al. 2011
• MEI_known_dbrip ==> Name of the pMEIs to be extracted from dbRIP (dbrip.org)
• MEI_known_1kproject ==> Name of the pMEIs to be extracted from Sudmant et al. 2015
• window_size ==> The range to consider from the mapping site
• mapq_bwa ==> bwa mapping quality cutoff
• blast_score_R1 ==> Blast bit score cutoff for Read1
• blast_score_ref ==> Blast bit score cutoff for reference MEIs
• primer_position ==> [5|3], if the ME-specific primer is located on the 5' of the ME, input 5, if the ME-specific primer is located on the 3' of the ME, input 3.
• ME_fragment ==> the ME sequence that will be used for blast. xxx when file name is xxx_primer.fasta Caution: direction primer binding site to end of ME
• repeatcover ==> [on|off], if on is specified, Read2s which are 100% covered by known MEs will be removed.
• clustering_type ==> [fixed|flexible], clustering methods allowing fixed or flexible window note: ==> MEI_ref_RM, MEI_known_stewart, MEI_known_dbrip can allow multiple terms using regular expression e.g., MEI_ref_RM=AluYb8|AluYb9

<path>

• path_mescan ==> the location of ME-Scan tool
• path_samtools ==> the location of samtools for coverting bam to sam
• path_bwa ==> the location of bwa for mapping Read2 against the genome
• path_blast ==> the location of blast for filtering Read1
• path_liftover ==> the location of liftover for lifting previous known polymorphic loci (from hg18 to hg19)
• path_sort_temporary_directory ==> the location for temporary files
• path_python3 ==> the location of python3
• path_primer3 ==> the location of primer3
• path_bedtools ==> the location of bedtools
• path_primer_thermodynamic_parameters ==> the location of the parameter file for Primer3