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In tophat paper, there are 3 parameters to control the IUM reads mapping procedure.
k: 2k is the index length for IUM reads
s: length for index region of IUM reads
and a parameter for mismatches of extending out of the seed region.
However, in the tophat manual, it seems that there are no corresponding parameters. Parameters such as -a/--min-anchor-length and -m/--splice-mismatches do not function as 3 parameters described in the paper.
Do I have any misunderstanding for the tophat manual or paper? If there are indeed no parameters like k, s and something for mismatches, how can I adjust the behavior of tophat for different reads length?
k: 2k is the index length for IUM reads
s: length for index region of IUM reads
and a parameter for mismatches of extending out of the seed region.
However, in the tophat manual, it seems that there are no corresponding parameters. Parameters such as -a/--min-anchor-length and -m/--splice-mismatches do not function as 3 parameters described in the paper.
Do I have any misunderstanding for the tophat manual or paper? If there are indeed no parameters like k, s and something for mismatches, how can I adjust the behavior of tophat for different reads length?