I'm quite new to bioinformatics and am currently running into a dilemma on how to approach my re-mapping. I have successfully assembled my FASTQ-files (reads) and now have my contigs in FASTA files. From these FASTA-files, I want to predict its genes (with Prodigal) and find the depth (abundance) of the predicted genes. However, I am unsure if I should re-map my contigs back to my reads first, or if I should gene predict first, and then re-map the predicted genes back to the reads. As I see it, by re-mapping the predicted genes, I risk losing some of the reads not entirely in the gene. However, by re-mapping the contigs, I get a depth for all the reads on the contig, but will then have to correlate that data to the predicted genes somehow. Do you have any suggestions or preferences? And if you do, why would you choose one over the other.
Thank you very much in advance!