Hi, I would like to know if it is possible to use GATK on small RNA seq using the RNA seq processing.
No, you will not be able to use GATK with small RNA-seq data. There may be a few obstacles to overcome.
1) The sequence is so small and GATK is tested on longer reads
2) Aligning the reads to a reference is very difficult
3) You will need a transcriptome which may be hard to find if you are working with a non-model organism