I want to make a many bam alignment files with various mapping rate.
For it, I choose the SimSeq program which makes a Synthetic short reads from reference input data.
But I should make errors of a various level, because my objective is to make alignments with various mapping rates (ideally 0% to 100%, or 0.xx% to 8x.xx%).
In the manual of SimSeq program, I can make an error with option -e or --error <arg>. "If simulated read error desired, path to read error file."
But I don't know what the read error file is. Can you give me the example of is? what is the filename extension of this?
Oh, if you have an idea what it exactly means the 'duplication rate' option("probability of generating a duplicate."), please tell me what it makes really.... Firstly I misunderstand that this duplication rate option can make the various mapping rate and the result was that all alignment data have about mapping rate of 89%...T.T
.
Thanks.
