Currently, I have BAM files sent to me (I have acces to fastq files as well if that is a required data) from a sequencing company, and generated a count matrix using RSubreads package function, featureCounts(). I have also ran DESeq2 through the count matrix and produced a filtered list of significant DEGs. However, I am noticing that there are a fair portion of the DEGs do not correspond to mRNA transcripts.
My question is, is there a way during the alignment process to label the reads being counted. For example, for gene X is a protein coding gene based on a reference annotation, and once the count table is generated, there some meta data column or output denoting the type of gene X. Ultimately I want to be able to select the types of genes being analyzed downstream, e.g. mRNA.
Thank you in advance, Yeeshouw Wang