rcorrector_paper
#scripts: You can find the scripts used in the evaluation in the subdirectory "scripts".
In the manuscript, we have 4 data sets, the scripts for them are in the subdirectories "simulate_pair_100M", "peach", "lung", "geuvadis".
For each data set, to run each error corrector, you can go into the corresponding data set directory and execute run_"tools_name".sh . For example, if you want to run rcorrector, you can run "sh run_rcorrector.sh". You may need to change some paths in the shell script.
To append the "exp=xxx" tag in the simulated data set, you can run: "perl ../Tools/AddExpLevel.pl mason_read1.fq pro_file_from_fluxsimulator.pro> simulated_pair_100M_read1.fq" and also for the other mate pair read file
To evaluate the accuracy on the simulated data set, you need to compile the code in MasonVerify by "g++ -o verify verify.cpp". And the "run_verify.sh" script will output the accuracy for each setting.
For those programs, you can execute the script run_"program_name".sh .
The code to obtain the perfect alignments and compute the false positive rate are contained in "scripts/${data_set}/evaluate_tophat2_FP.sh"
We use the program "memusage" to evaluate the memory usage of programs. It is downloaded from musket repository and should be compiled by "g++ -o memusage memusage.c" before using.
#commit: git add .
git commit -m"Mesages"
git push -u origin master
#update git pull