I had previously worked with transcriptomic data containing microRNA info. My understanding was that the read count file I obtained from a public dataset contained miRNA names as rownames.
Now, while actually trying to create a read count file from fastq file, I realise that the final read count file should contain the names of corresponding DNAs, and not the original rna transcripts.
So my understanding is : for rna sequencing of coding RNAs, the read count file would contain as rownames the corresponding DNAs. However, if the read count file is for non-coding RNA, then the rownames will be the RNA transcripts themselves. Both these types of read count files are considered to be transcriptomic data
Is this understanding correct ?