CARNAC-LR howto and experiments from manuscript

Scripts require c++11 and Python3. CARNAC-LR is available at https://github.com/kamimrcht/CARNAC-LR

Experiment 1 - ring of cliques

The ring of clique file can be found here.

Command line

./CARNAC-LR/CARNAC-LR -f input_K7.txt

Output file

CARNAC-LR output this file: carnac_clique_ring.txt.

Each line of the output file is a cluster composed of 7 nodes that form a clique in the original file. CARNAC-LR successfully retrieves the 30 cliques that are 30 communities in this toy example.

Experiment 2 - comparison to state of the art

10K reads from chromosome 1 were extracted from full mouse transcriptome sequence.

"Ground truth" clusters we deduced from mapping results on mouse reference genome GRCm38 are accessible here.

Minimap and clustering

Minimap version 0.2 is used to compute overlaps between reads: minimap -Sw2 -L100 -t10 reads_10k.fa reads_10k.fa > minimap_10k_chr1.paf

PAF file is converted to an input graph: python3 ~/CARNAC/scripts/paf_to_CARNAC.py minimap_10k.paf input_graph_10k.txt

PAF file and input graph are found here: minimap_10k.paf/input_graph_10k.txt. Then all methods are launched on the input graph.

CARNAC-LR command line: ./CARNAC-LR/CARNAC-LR -f input_graph_10k_chr1.txt

Output files

PAF file and input graph are found here : minimap_10k_chr1.paf/input_graph_10k_chr1.txt.

Results command lines

Any result is obtained using scripts: validate_jaccard.py/validate_clustering

Command lines:

python3 validate_jaccard.py ground_truth_file clustering_output_file

./validate_clustering ground_truth_file clustering_output_file

For instance:

python3 validate_jaccard.py clusters_10k_chr1.truth carnac_10k_chr1.txt

./validate_clustering clusters_10k_chr1.truth carnac_10k.txt