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What is LSC?
LSC is a program written entirely in python2.6 that is able to correct the thrid generation long reads by the second generation
[ LSC 0.2.4 ] What is in the folder "output_old"?
I got three folders output, output_old, and temp.
I guess LSCoutput is new vision result and LSCoutput_old is earlier vision result. Right?
New result folder has new files like newLS.fa etc.
Could you explain the files mean?
The folder output_old contains some "old" results which may have slightly lower accuracy.
In LSC 0.2.4, I corrected some bugs and output "new" results in the folder output. You should use these files. newLS.fa is just a temp file for debugging. you only need to use full_LR_SR.map.fa and corrected_LR_SR.map.fa
LSC 0.2.1 runs fine on a small set of data, but when it runs on the whole short read set (49 GB) I get an read error in awk:
(awk: read error (Bad address)
At first try it reached 30 GB but this error popped up earlier and earlier with each run. This error also appears when I just run awk from the commandline on this set.
The user may have used mawk that is a very fast AWK implementation by Mike Brennan based on a byte code interpreter. You will install GNU awk to run LSC.