bowtie2 and then HISAT2? What does it mean in Data processing details on a paper?

Question

[Simon Ahn]

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?

[Chris Dean]

It was probably an oversight. It looks like the data was made publicly available two years prior to the publication. A lot of things can change during that time. Have a look at the methods described in their published paper and see if that clears things up (see Section 4.2).

Answer 1

[Philipp Bayer]

IMHO that must be a mistake: the data seems to be RNA so I would've directly gone for TopHat2 (or HISAT2).

(Unless they wanted to run Fastqc in BAM, not fastq mode - in which case Tophat2's bam would've worked too?)