I have pseudo-aligned some RNASeq reads using Kallisto where each sample was split over two flow cells.

I pseudo-aligned the fastq files for each flow cell separately, meaning for each sample I have two abundance TSV files that look like this:

target_id           length  eff_length  est_counts  tpm
ENST00000434970.2   9       7           0           0
ENST00000448914.1   13      11          0           0
ENST00000415118.1   8       6           1           0
ENST00000631435.1   12      10          0           0
ENST00000632684.1   12      10          0           0

I would like to merge each sample's two TSV files into one and aggregate the transcript level counts to gene-level counts with tximport in R.

I'm unsure about the best way to approach this. The length column is the same in both TSV files, and the est_counts just need to be added together, but I'm not sure about eff_length and tpm. Does tximport require this information?

I would appreciate some advice.

Thank you!