FLAME: Full-Length Adjacency Matrix Enumeration.

FLAME:fire: is a long-read splice variant annotation tool.

PubMed - Journal

FLAME has two modules:

• Gene Specific FLAME:
  • Filtering, translation, quantification of splice variants and exon connectivity through an Adjacency Matrix
  • Detection of novel exons sites or exon variants through frequency
  • Confirmation of said novel exons sites through the use of:
    • Detection of possible adjacent splice site signals
    • Short-read sequencing reads
• FLAME-GLOW:
  • Global gene iteration
  • Filtering and flagging of genes with incongruent annotations
  • Translation and quantification of genes with sufficient reference annotation

Requirements

• Python 3.6
• pysam

Installation

OS X & Linux:

git clone https://github.com/marabouboy/FLAME

FLAME usage example

• Gene Specific FLAME under minimal condition adheres to the following syntax:

  ./FLAME.py -I [INPUT.bed] -GTF [Annotation.gtf] -G [Gene]

  Minimal Gene Specific FLAME will run:

  1. create.ref
  2. filter
  3. translate
  4. quantify
  5. annotated.adjmtx
  6. frequency.site
  7. frequency.thresh
  8. incongruent.adjmtx

• Gene Specific FLAME with maximal condition adheres to the following syntax:

  ./FLAME.py -I [INPUT.bed] -GTF [Annotation.gtf] -G [Gene] -R [Reference.fasta] -B [Shortread.bam]

  Maximal Gene Specific FLAME will run:

  1. Step i-viii of Minimal Gene Specific FLAME
  2. splice.signal
  3. shortread

• FLAME-GLOW

  ./FLAME.py -I [INPUT.bed] -GTF [Annotation.gtf]

• If there is any other questions regarding the use of FLAME, refer to our Wiki

Flags

• General FLAME Flags:

  -I [INPUT.bed]:             #Input file in BED12 format (Required)
  -GTF [Annotation.gtf]:      #Reference annotation file in GTF format (Required)
  --range [int]:              #Variance function window range (Optional, with default = 20)
  -O [string]:                #Output prefix (Optional, with default = "Flame-")

  • Gene Specific FLAME Flags:

    -G [Gene]:                  #Target gene (Required)
    -R [Reference.fasta]:       #Organism reference assembly sequence in fasta-format for the splice.signal-funciton (Optional)
    -B [Shortread.bam]:         #Short-read RNA sequencing data in bam- or sam-format for the shortread-function (Optional)
    --verbose                   #Optional Flag to output additional files (Optional)

  • FLAME-GLOW Flags:

    --min [int]:                #Minimum read coverage (Optional, with default = 10)
    --ratio [float]:            #Minimum annotation ratio for the FLAME-GLOW module (Optional, with default = 0.25)

Test Running FLAME

There is currently only toy data for the Gene Specific FLAME module.

Both the data as well as instruction for how to run the Gene Specific FLAME module exists under the Data directory

Release History

• 0.1.4
  • Fixed smaller bugs in GLOW-mode.
• 0.1.3
  • Fixed smaller bugs
  • Added a Wiki
• 0.1.2
  • Updated README.md
  • Added toy data
• 0.1.1
  • FLAME-GLOW mode implemented
  • Beta-version
• 0.0.1
  • Work in progress
  • Alpha-version

Meta

Alan Bäckerholm – Alan.baek1@gmail.com

Distributed under the MIT license. See LICENSE for more information.

https://github.com/marabouboy/

Contributing

1. Fork it (https://github.com/marabouboy/FLAME/yourfork)
2. Create your feature branch (git checkout -b feature/fooBar)
3. Commit your changes (git commit -am 'Add some fooBar')
4. Push to the branch (git push origin feature/fooBar)
5. Create a new Pull Request