I did some ribosomally depleted RNA-seq in rat brain. Does anyone have recommendations on how to quantify/compare small RNA expression between samples? I have used RNA STAR to map reads back to the genome and determine reads per gene for mRNA, but I can't seem to repeat that for any kind of small RNA like lncRNA or miRNA and the pipeline keeps failing. Is there a specific GTF file or similar type that I should be using? Do I need a different pipeline? Help please!
Hi, Max!
In rRNA depleted libraries I believe you won't identify small RNA because probably the RNA fragments used to build the libraries were greater than you need to this.
However, to identify and quantify long noncoding RNA (lncRNA), you need a reference genome or transcriptome with this type of RNA. I've never worked with the rat genome, so I don't know what the annotation is like for that species.
The pipeline to quantify mRNA and lncRNA are the same, using the same reference genome. If you are not finding any lncRNA in the BAM file generated by STAR, it may be that this type of gene is not in your reference genome or that it has simply not been expressed in the condition you are studying.
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