I am still working on the DEG analysis of miRNA.
I have sucessfully trimmed out the adapter and index sequences and mapped them using bowtie2.
Then, I have used samtools to convert sam file to bam file.. and finally got the .bam files.
Here, I mapped our fastq file to mouse whole genome reference file instead of mirBase hairpin. fa file..
(mapping rate is around 90%)( Note I have 6 samples including 3 controls)
For DEG analysis of miRNA( differentally expressed miRNA), I am trying to use cufflink-cuffdiff pipeline.
By accident, I did not put the -g genes.gtf option.
> cufflinks -p 4 -g genes.gtf -o xxx_clout xxx.bam
when, I put the "-g genes.gtf" option (since I want to annotate our result), my genes.fpkm_tracking file have 25000 genes with annotation .
When, I put the command without -g genes.gtf option ,
my genes.fpkm.tracking file has 1829 lines. (annotation.. e.g. CUFF.1 CUFF.2 ..... CUFF.1829)
Could you please someone let me know why these two files are so different even the different is only "-g genes.gtf " option??