Hello all,

I am working on the differentially expressed microRNAs analysis.

I have used the bowtie2-cufflink-cuffdiff pipeline. (for the reference I downloaded from UCSC site)

I have two questions.

1. When running cufflinks, I have ran two ways (with -g xxx.gtf option, without -g option). I know it should only makes small difference. But results look somehow different. Especially, the fpkm value as well as the status of significance. So, I will get different DEGs based on the existence of -g option. Does it make sense?
2. Second, even though it is the fastq file of miRNAs, from the output file gene_exp.diff of cuffdiff, I can see some of reads are mapping to genes instead of miRNAs.. I may guess it is true since our experimental data can have some of mRNAs even though it intends to include microRNAs. Among 83 significantly differentially expressed ones, only 27 are mapped to microRNAs. Is it reasonable number? Or Do I miss something?