I Hope I am posting in the right section. I am sure this question has been asked several times before and I have been going through discussion on similar topics on Biostars but I am still confused and hoping I could get a more simple answer based on my beginner level in NGS data analysis.
I am trying to perform miRNA-seq analysis. I Have ten samples. I performed adaptor removal and trimming of reads using FastX toolkit. Now I have reads ranging from 17 to 44 nucleotides. I then used these file as input for bowtie and mapped my samples to hg19. I now have SAM file for each sample.
What I want to do next is :
1. Distribution/composition analysis of reads according to their size. i.e how many reads are of length 20,21,22 and so on. So I could make a bar plot or graph.
2. To find out which and how many reads in my samples map to GenBank entries and rFam database (rRNA, scRNA, snoRNA, snRNA and tRNA).