Global stability analysis and direct numerical simulation (DNS) are used to study boundary layer flows with an isolated roughness element. The aspect ratio of the element (
$\eta$
) is small, while the ratio of element height to displacement boundary layer thickness (
$h/\delta ^{*}$
) is large. Both steady base flows and time-averaged mean flows are able to capture the frequencies of the primary vortical structures and mode shapes. Global stability results highlight that although the varicose instability is dominant for large
$h/\delta ^{*}$
, sinuous instability becomes more pronounced as
$Re_h$
increases for the thin geometry (
$\eta =0.5$
), due to increased spanwise shear in the near-wake region. Wavemaker results indicate that
$\eta$
affects the convective nature of the shear layer more than the type of instability. DNS results show that different instability mechanisms lead to different development and evolution of vortical structures in the transition process. For
$\eta =1$
, the varicose instability is associated with the periodic shedding of hairpin vortices, and its stronger spatial transient growth indicated by wavemaker results aids the formation of hairpin vortices farther downstream. In contrast, for
$\eta =0.5$
, the interplay between varicose and sinuous instabilities results in a broader-banded energy spectrum and leads to the sinuous wiggling of hairpin vortices in the near wake when
$Re_h$
is sufficiently high. A sinuous mode with a lower frequency captured by dynamic mode decomposition analysis, and associated with the ‘wiggling’ of streaks, persists far downstream and promotes transition to turbulence. A new regime map is developed to classify and predict instability mechanisms based on
$Re_{hh}^{1/2}$
and
$d/\delta ^{*}$
using a logistic regression model. Although the mean skin friction demonstrates different evolutions for the two geometries, both of them efficiently trip the flow to turbulence at
$Re_h=1100$
. An earlier location of a fully-developed turbulent state is established for
$\eta =1$
at
$x \approx 110h$
.