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README.md

CARNAC-LR (Clustering coefficient-based Acquisition of RNA Communities in Long Reads)

Get CARNAC:

git clone https://github.com/kamimrcht/CARNAC.git

Requirements

  • C++11 and GCC version from 4.9 / CLANG from 3.9
  • Python3 for scripts

Compilation and Usage:

cd CARNAC;
./install;

Warning:

For MacOS users (clang version < ), the flag -fopenmp must be removed from Makefile before the compilation. In this configuration CARNAC cannot be run with several threads.

Usage:

./CARNAC-LR -f input_file (-o output_file -t nb_cores)

Quick test:

./CARNAC-LR -f test/test.input

The result clusters should be the same than in test/final_g_clusters_to_obtain.txt

Options:

./CARNAC-LR

to output the options

  • -f is mandatory
  • -t gets the number of threads (default 2)
  • Output is written in final_g_clusters.txt by default (-o to change output name)

I/O:

Input format:

Example with example_file.paf and reads.fa:

python3 ./scripts/paf_to_CARNAC.py example_file.paf reads.fa input_CARNAC.txt
./CARNAC-lR -f input_CARNAC.txt -o output_CARNAC.txt

Output format:

Reads are attributed indices from 0 to #reads-1 in order of appearance in input file. The output is a .txt file with one line per cluster, with the indices of its read members separated by spaces. For instance with 6 reads in the input in the previous example:

less output_CARNAC.txt
0 1 2 3
4 5

The first four reads are in one cluster, the two last reads are in a second cluster. Transform clusters file to separated Fasta files:

./scripts/CARNAC_to_fasta <original_read_file.fa> <CARNAC_clusters_files> [cluster_min_size]

Mandatory arguments are the output of CARNAC followed by the read file. Clusters are output in fasta format, with a file name that correspond to their order of appearance in CARNAC's output. A A minimum size of the clusters to be written can be set.

Contact:

camille.marchet@irisa.fr