My RNA-Seq data is in format of fastq(ungzipped from fastq.gz format).I used STAR 2.5.3a mapping the reads with already indexed reference genome. It seems good. But I found the size of generated SAM file is strange. My original input fastq data is like 1.3-1.5 GB, but the SAM file ranges from 3.8 GB to 4.5 GB. Is that normal? If not, what is something wrong there?
A SAM file will typically be larger than a FASTQ file because, in general, it contains all the information of the FASTQ plus a lot of other information.
In addition, each FASTQ record may produce more than one alignment, hence you can see how it could easily grow to be much larger than the original data.