Metadata-Version: 2.1
Name: RNA-APoGee
Version: 0.0.8
Summary: A package for aligning RNA-seq data without reference biases
Home-page: https://git.illumina.com/spanag/APoGee
Author: Sofia Panagiotopoulou
Author-email: spanagiotopoulou@gillumina.com
License: UNKNOWN
Description: # RNA-APoGee
        
        RNA-APoGee (RNA Alignment to Personal Genomes) is a package to align RNA-seq data while
        minimizing reference biases. It can also be used to align RNA-seq data to haplotype resolved variants.
        Currently, RNA-APoGee relies on the Olego aligner, although
        other aligners could be used instead.
        
        ## Pre-requisites:
        - RNA-APoGee has only been tested on Linux and requires Python 3.
        - [Olego](https://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation) must be installed and on your PATH.
        - [samtools](http://samtools.sourceforge.net/)
        
        ## Installation
        ```pip install RNA-ApoGee```
        
        ## Command line utilities
        Alignment involves two steps:
        1. Generating a "personalized" genome that has the variants of the
        individual embedded into the reference genome.
        2. Aligning against the reference and the personal genome (or against two haplotypes) and then merging
        the two sets of alignment to pick the best alignment for each read.
        
        ### Generating a personal genome
        
        `create_genomes` creates versions of an input FASTA with sample-specific SNVs replacing
        reference bases.
        
        If you have phased variants, you can create two 
        VCFs corresponding to the variants of each haplotype and then create two versions of
        the reference by calling `create_genomes` twice, once for each haplotype
        (unfortunately currently this script ignores the phasing of the variants.)
        
        ```
        create_genomes --fasta FASTA
                       --vcf VCF
                       --outdir OUTDIR
                       [--samples SAMPLES]
                       [--min_gq MIN_GQ]
                       [--chunk CHUNK]
        
          --fasta FASTA      FASTA file that will be used as the base for generating
                             personal genomes. For each sample in the input VCF, an
                             individual genome will be created by substituting the
                             sample's SNVs into this base FASTA. SNVs will be
                             considered only if the FILTER field is PASS, and the
                             genotype quality is greater than <min_gq>.
        
          --vcf VCF          VCF with variant calls. Can have multiple samples.
        
          --outdir OUTDIR    Personal genome for sample <sample> will be in
                             <outdir>/<sample>.fa
        
          --samples SAMPLES  (Optional) Comma separated list of samples from the input VCF. If
                             provided, only the personal genomes for these samples
                             will be created, otherwise personal genomes for all
                             samples in the input VCF will be created.
        
          --min_gq MIN_GQ    (Optional) Minimum genotype quality to consider a variant
        
          --chunk CHUNK      (Optional) How many bases to keep in memory. Reduce if running OOM.
        ```
        
        ### Aligning against the reference and the personal genome
        
        `apogee` aligns RNA-seq data to a personalized genome. Each read (or read-pair in case
        of paired data) is aligned against two FASTAs (correponding to two haplotypes
        or to a reference with and without an individual's variants). Then for each
        read (or read-pair) the best alignment across the two FASTAs is chosen. The
        order in which the two references are given (i.e. which one is specified as
        `ref_fasta` and which one is specified as `alt_fasta`) does not matter. Note
        that a lot of intermediate files are created. If `tmp_dir` is specified, all
        intermediate files will be stored there, with a prefix matching the prefix of
        the output BAM. In this case, it's up to you to delete that directory. If
        `tmp_dir` is not specified a temporary directory will be created, in the same
        directory as the output BAM and then deleted (so all intermediate files will be lost).
        
        ```
        apogee --fq1 FQ1
               --ref_fasta REF_FASTA
               --alt_fasta ALT_FASTA
               --bam BAM
               [--fq2 FQ2]
               [--tmp_dir TMP_DIR]
        
          --fq1 FQ1              FASTQ file with all reads (for single-end) or read1
                                 reads (for paired-end)
          --fq2 FQ2              (Optional) FASTQ file with read2 reads
          --ref_fasta REF_FASTA
                                 First FASTA against which to align
          --alt_fasta ALT_FASTA
                                 Second FASTA against which to align
          --bam BAM              Output BAM
          --tmp_dir TMP_DIR      (Optional) Directory of intermediate files
          --threads THREADS      (Optional) Number of threads for alignment [1]
        ```
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
