HEy All,
I have few paired small RNA seq plasma samples. I did all the quality control, trimming, mapping and quantification for the case and control samples. Now i am trying to know the number of reads mapped to all differnet non coding small RNA species (microRNA, scRNA, snoRNA, snRNA, rRNA, tRNa). All i want to know if that if look at the gtf file, everything starting with mir is all the microRNAs, so i can easily count those. Can anyone tell me about scRNA, snoRNA, snRNA, rRNA and tRNa. I see SCARNA and SNAR in the list also.
What genome and which GTF file? If it is from a public source then provide a link for the file.
snoRNA snRNA scRNA SCARNA
You should know what rRNA and tRNA are.
Well i have used Homo_sapiens_UCSC_hg19 genome and used the gene.gft file from archive-2015-07-17-14-32-32.
ya ofcourse rRNA and rRNA are the non coding trancriptional RNAs, sorry exclude these.