Recently I want to run Trinity de novo assembly for a bacterial community transcriptomics study. I started a job with Trinity with yes option for “Are you pooling sequence datasets?” and used all my forward read files for left/forward reads options and reverse reads for right/reverse reads option. However, recently I have been reading the forums and they suggested to concatenate the read files first before running Trinity. Do both options give the same result or are there differences in what the pooling option does as opposed to concatenated data?
Yours sincerely,
Wei Jie