I have previously worked directly with read counts files, but this is my first time trying to generate read count from fastq files.
QIAseq miRNA Library prep was used for the experiment. (I was not the one who performed the library prep. I just received the fastq files)
Reading few tutorials and following http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html, Salmon seems to be the state of the art method for generating read count files. My project is specifically focused on small non-coding RNAs.
Can someone please help me with these questions ?
- I'd want to identify specific sncRNA as biomarkers (something like miR-182-5p is increased for cancer patients). So is it necessary to create read count files with rownames as genes ? Can read count files with sncRNAs as rownames be directly created ? (rather than first creating one with genes and then mapping it to sncRNAs with something like miRBase)
- Is Salmon (following the steps in the link above) recommended for quantifying sncRNAs ? https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4869-5 specifies that alignment-free tools are not ideal for small RNAs