Mutual-pepino

In this repository we will attempt to reproduce a research pipeline that employs a heuristic pairwise alignment algorithm to perform differential expression analysis on Sea Cucumber genetic samples, more specifically on regenerative intestinal tissue samples vs. non regenerative ones.

Files:

• dbg_optimized.py:

  • Usage:

     $ python3 dbg_optimized.py -k <k-mer lenght> -A <fastq A> -B <fastq B> -o <outputfilename> 

  • Ouput:

    • GFA encoded graph with differential expression information anotated

     H	VN:Z:1.0
     S	0:0:(A:1,B:1)	AAGTTGCGCTAGGGTTAAACT
     S	0:1:(A:1,B:1)	AGTTGCGCTAGGGTTAAACTC
     L	0:0:(A:1,B:1)	+	0:1:(A:1,B:1)	+	20M

• analysis.py:

  • Usage:

     $ python3 analysis.py -f <filename> [-t <threshold>] [-o <outputfilename>]

  • Ouput:

    • GFA encoded link with differential expression more than or equal to threshold, plus differential expression coeffient.

     L       0:0:(A:1,B:1)   +       0:1:(A:1,B:1)   +       20M
     Differential Coefficient: 0.0

Worked continued on the DBGDE repository.

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Proposed (DONE) Workflow:

• Build De-bruijn Graph:
  • Used this approach.
• Counted the proportion/distribution of kmers recovered from each organism.
• Perform differential analysis on that data

Collaborators:

• Dr. Humberto Ortiz-Zuazaga
• Kevin Legarreta
• Louis Gil
• Israel Dilán-Pantojas