I am new to salmon. Got 26% mapping rate with one set and 43% with another. Rest of samples have more than 75%. Although all the data have similar quality and all have adapter content empty in FASTQC. The quality is almost above 30 but with few bases at the beginning less than 20 but greater than 10. I did not trim them, read about how aggressive trimming is bad.
I also changed the k index during building the index. Changed the reference transcript. Same results. I blat the over representative sequences and found no contaminants. I mapped the sample that has salmon 26% with Tophat default parameters, got 73% alignment. Not sure why?
Not sure what else I can do? I can't ignore the 26 and 43% samples from the analysis. They are important.