Indels and Alignment-based mode

[John Ma]

When STAR writes alignments in transcript coordinates, it can be with or without indels or softclips. The former is STAR's default since rsem only accepts BAM files without indels. Does Salmon require any one type?

Thanks for the answer in advance.

John Ma
Postdoctoral Fellow
Department of Lymphoma/ Myeloma
UT MD Anderson Cancer Center
Houston, TX, USA