I post this question because I only found old information in the forum. I am working with a transcriptome that don't have an important (for my work) gene annotated, but this gene is in the GenBank. So, my question is, What is the best way to do the mapping against this gene?
Now I am testing HISAT2, but it is slow and it seems that it is mapping wrong some sequences. The files that it is produce are too long compare to the mapping against to all genome. I have read on this forum that many mappers can give false positives if the mapping is not done against the entire genome. This is because they give the reads that map with a certain score, even if the alignment is imperfect. Is there a mapper that can control this?
I suppose another alternative would be to try to locate this gene in the assembled genome file, modify the annotation file and do the mapping and other parts of the process with the modified files. What program or approach would be better to locate the gene in the genome? minimap2, blastn ...?