TopHat [ 58] was used to map reads against the Plasmodium chabaudi chabaudi AS reference genome [ 33], with maximum intron size set to 10000 and inner-mate distance set to 100.
Sequence reads were mapped to Arabidopsis thaliana TAIR10 [ 42] genome using TopHat v2.0.9 [ 43] with default parameters, except of maximum intron length set at 5,000.
By further analyzing the conserved intron set, we found 2,753 cases of intron loss and 778 cases of potential intron gain; 19,444 introns had remained perfectly stable.
However, in the Acc. Intron set, this is only true when considering the subset of introns previously identified as accelerated.
Default settings were utilized except for the following modifications: the minimum intron length was set to 50 nucleotides, the maximum intron length was set to 250 000 nucleotides, the minimum isoform fraction was set to 0.10, and only uniquely mapping reads were maintained (max-multihits was set to 1).
The maximum intron length was set to 6000 bp and other parameters were left as defaults.
For yeast datasets the maximum intron size was set to 5,000.
The minimum and maximum intron sizes were set to 20 bp and 409 600 bp for all approaches.
The maximum intron size is set as 10% longer than the longest intron evidenced by the transcript alignment, unless this value is greater than 5,000, in which case the maximum is limited to 5,000.
For all tests, the minimum intron size, n, was set to 40; the maximum intron size, x, was set to 5000; and the minimum chunk size, c, was set to 6, while the MICS, i, was varied.
