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wgsim_eval output clarification
I am an undergraduate student just starting in bioinformatics and my boss has asked me to use wgsim to get a better sense the differences between bowtie2 and BWA. We've run the simulated data through our pipelines to generate sam files and used the commands
wgsim_eval.pl alneval -ag50 filename.sam
wgsim_eval.pl alneval -g50 filename.sam
on each sam file. From another thread I assumed that the column headers when the -a option is used mean: mapping quality threshold, number of mapped reads with a mapping quality no less the the first column and number of mis-mapped reads.
Could someone please expand on what these column headers mean, what the column headers are when the -a argument is not used, what the -a option actually means (it does not seem to be documented) and finally how ROC curves like those found here were generated from wgsim_eval data.
Thank you very much!
wgsim_eval.pl alneval -ag50 filename.sam
wgsim_eval.pl alneval -g50 filename.sam
on each sam file. From another thread I assumed that the column headers when the -a option is used mean: mapping quality threshold, number of mapped reads with a mapping quality no less the the first column and number of mis-mapped reads.
Could someone please expand on what these column headers mean, what the column headers are when the -a argument is not used, what the -a option actually means (it does not seem to be documented) and finally how ROC curves like those found here were generated from wgsim_eval data.
Thank you very much!