Could anyone comment on appropriate species-specific adaptation of min-coverage-intron and max-coverage-intron default values?
I have calculated, using a reference annotation, the minimum and maximum intron values corresponding to my organism. However Tophat has 3 groups of intron settings; and coverage-intron has defaults distinct from segment-intron and intron-length, and I am wondering what the significance of that is.
It seems to me that all 3 groups of intron settings, coverage-intron included, should use the calculated intron value, as each contributes to information used to call introns & corresponding splice junctions ab inito.
Alex
I have calculated, using a reference annotation, the minimum and maximum intron values corresponding to my organism. However Tophat has 3 groups of intron settings; and coverage-intron has defaults distinct from segment-intron and intron-length, and I am wondering what the significance of that is.
It seems to me that all 3 groups of intron settings, coverage-intron included, should use the calculated intron value, as each contributes to information used to call introns & corresponding splice junctions ab inito.
Alex
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