How abundance calculation is done for the genes which are annotated by any reference database like MegaRes, contig file generated after de novo gene assembly is aligned to the database using Blast. Is the abundance referred to the number of contigs annotated as a specific gene or is it some other way??
The abundance calculation for genes annotated by a reference database such as MegaRes depends on the specific approach used for gene quantification. In general, the most common method involves mapping the sequencing reads to a reference database and then counting the number of reads that map to each gene.
In your case, it sounds like you are using a de novo gene assembly approach to generate contigs, which are then aligned to the MegaRes database using BLAST. To quantify the abundance of each gene, you could count the number of contigs that align to each gene in the database. However, it is important to keep in mind that the number of contigs is not necessarily directly proportional to the expression level of a gene, as different genes may have different lengths and levels of expression.
A more accurate approach to quantifying gene expression would be to use tools such as RSEM, Kallisto, or Salmon, which use a statistical model to estimate the expression level of each gene based on the mapping of the sequencing reads. These tools take into account the differences in gene length and the potential for reads to map to multiple genes, which can improve the accuracy of the abundance estimation.
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