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Old 09-20-2012, 07:13 AM   #19
Senior Member
Location: USA, Midwest

Join Date: May 2008
Posts: 1,155


I would really like to use your software but it is extremely difficult to do so given the complete lack of documentation. The 'How it works?', 'Tutorial', 'Manual' and 'Filters' links are website are dead links. The 'FAQ' has just one line referring to SpliceMap. There isn't even a README file. Yes I can run the program but without any documentation I have know idea whether my results are correct or meaningful.

I installed LSC and ran it against a PacBio long read data set consisting of 100,000 reads, totaling 38Mbp. My short read set are 20 million, 100bp Illumina reads. I ran the program with default parameters and the output generated is 3 files,, and Each file contains ~30,000 reads; the full file contains ~15Mbp and the other two each ~8Mbp.

What am I to make of these files? Does this output sound normal? Which output file is useful for further analysis?
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