My data consists on 3 RNA-seq datasets and a non-model genome. I ran Trinity on each dataset to produce the transcripts, and afterward, I wanted to align the transcripts to the genome so that are correctly mapped (and in the end used as experimental evidence for annotation). Unfortunately, GMAP had an unstoppable increase in RAM use, and even when trying to correct the memory usage, the program couldn't align any read.
I would like to know if there's any alternative that could map the transcripts data to the genome. I've seen that STAR and BLAT are sometimes mentioned, but I ignore if they can be used in the same way as I intended with GMAP.
I really appreciate any help that can be provided.