The aa-aligner's intro from buchkovm

AA-ALIGNER: Allele-Aware ALignments for Investigating GeNetic Effects on Regulation

Enrichment of one allele in quantitative sequence data, or allelic imbalance, can indicated allelic differences in transcription factor binding and/or gene transcriptional regulation. Reference mapping biases at heterozygous sites hinder accurate identification of allelic imbalance. We have developed the AA-ALIGNER pipeline to overcome reference mapping biases and identify allelic imbalance in quantitative sequence data. AA-ALIGNER can accurately identify imbalance using any available or even no sample genotype data.

AA-ALIGNER 1.0 - AA-ALIgNER for a single machine usage: perl AA_ALIGNER.pl [options]... [fastq files(s)] GENERAL OPTIONS: -configuration_file configuration file (required) -out_directory directory for permanent files (default=./) -temp_directory directory for intermediate files (default=./) -out_prefix prefix for output bam file and imbalance files

RUN OPTIONS: -create_reference create a sample-specific reference genome (default=OFF) -filter_fastq filters fastq files before alignment to convert base qualities to Sanger format, trim sequences (if necessary), and removes low quality sequence reads (default=OFF) -align aligns sequences to specified genomes (default=OFF) -filter_alignment filters alignments to remove reads that map multiple sites,fall in blacklist regions, and are possible PCR duplicates (default = OFF) -find_imbalance dentifies sites allelic imbalance in sequence alignment (default=OFF) -all runs entire alignment pipeline filter_fastq, align, filter_alignments, and find_imbalance (default=ON)

AA-ALIGNER CLUSTER 1.0 - AA-ALIGNER for a cluster (currently implemented for LSF only) usage: perl AA_ALIGNER_cluster.pl [options]... [fastq files(s)] GENERAL OPTIONS: -configuration_file configuration file (required) -cluster_configuration configuration file for cluster settings -out_directory directory for permanent files (default=./) -temp_directory directory for intermediate files (default=./) -out_prefix prefix for output bam file and imbalance files

RUN OPTIONS: -create_reference create a sample-specific reference genome (default=OFF) -filter_fastq filters fastq files before alignment to convert base qualities to Sanger format, trim sequences (if necessary), and removes low quality sequence reads (default=OFF) -align aligns sequences to specified genomes (default=OFF) -filter_alignment filters alignments to remove reads that map multiple sites,fall in blacklist regions, and are possible PCR duplicates (default = OFF) -find_imbalance identifies sites allelic imbalance in sequence alignment (default=OFF) -all runs entire alignment pipeline filter_fastq, align, filter_alignments, and find_imbalance (default=ON) Example Usage Create usage examples are given for AA_ALIGNER but also apply to AA_ALIGNER CLUSTER with the addition of the cluster_configuration option

FASTQ Files used in the example can be found in AA_ALIGNER/example/fastq/ Create a custom reference file

System Dependencies GENERAL Perl https://www.perl.org/

Perl Modules: Getopt::Long Math::CDF

Java https://java.com/en/download/

Python https://www.python.org/

FASTQ FILTERING FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

GALAXY SOURCE for FASTQ_groomer https://wiki.galaxyproject.org/Admin/GetGalaxy

FASTX Toolkit http://hannonlab.cshl.edu/fastx_toolkit/

SEQUENCE ALIGNMENT GSNAP/GMAP http://research-pub.gene.com/gmap/

FILTER ALIGNMENT Picard Tools http://broadinstitute.github.io/picard/

SAMtools http://samtools.sourceforge.net/

FIND ALLELIC IMBALANCE SAMtools http://samtools.sourceforge.net/