Using pre-made software trying to implement Mutual software algorithm to get differential expression.
We will implement GFA1 working copy that will reconstruct the contig with links of it's kmers.
We have:
- One implementation trying to get GFA2 working at: https://github.com/Omig12/Mutual-pepino
- The one I just did is GFA1 with GFApy working and beign read by Bandage. Used segment for both fragment and the segment, the Segment appears first follow by the kmer subsegments.
Format of GFA1 Segment is: S id_of_original_segment contig.
Format of GFA1 subSegment is: S id_of_original_segment:subsegmentid:(A:count,B:count) kmer
Where id_of_original_segment is the same as first segment, subsegmentid is this kmer id, a tuple with the count of all the times that kmer appears in the organism.
An example to run the dbg.py is:
python dbg.py -k <kmer_size> -A <Organism A file(s)> -B <Organism B file(s)>