This is an data processing detail from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3056968. \ It says they used bowtie2, which is an alignment tool, and then used TopHat (now HISAT2), which is also an alignment tool. \ I have no idea why they aligned their reads twice. Is this just a mistake? or is there something that I don't know?