My Dear Expert Friends, Hi. ( I'm not native in English so, be ready for some possible language flaws).
I have read this topic, and it seems that "The Idea of that is to find novel sequences".
my question is this that which one is a better strategy for non-model animals RNA-seq to find novel sequences:
1- Running local blastn of transcriptome de-novo assembly against nt database
2- or aligning millions of reads against the NCBI nt database using BBMap
Please offer a short description that why you have chosen your preferred choice.
Thank you in advance.
Dear Brian Bushnell , Hi and thank you.
about the " use BBMap for just those reads that do not map to the transcriptome"
Do you mean to map them to nt database or mapping to some close species reference genome ?
I meant, map them to nt... but it really depends on what you're trying to accomplish, and whether you have reference genomes of related species. If the goal is to see if you have sequences that do not appear in nt, then mapping to nt would be the way to go.