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Old 07-09-2014, 07:56 AM   #1
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Location: America

Join Date: Jul 2014
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Default Tophat coverage-intron

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.

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Old 07-14-2014, 05:26 AM   #2
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Location: Berlin, Germany

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Hi Alex!

According to the manual, the values --min-coverage-intron and --max-coverage-intron are used only when --coverage-search option is activated. This is a special mode for Tophat, which uses alternative strategy to search for exons. One can read more here:

The values --min-segment-intron and --max-segment-intron are used in the main Tophat algorithm (which is based on segmentation of reads) to determine maximum size for intron and intron.

As I understand, the values --min-intron-length and --max-intron-length are used to finally filter and report introns found by both methods. In the source code they are used when the final reporting is performed and have names "--min-report-intron" and "--max-report-intron". If you are not using coverage search (it is disabled by default) then you probably have to set only the intron length restrictions from general options and perhaps those that are related to segment search.

Hope that helps!
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