Hi all,
I have data (illumina RNA-seq) from 14 different individuals, all trimmed and quality-checked with Fastqc. When I run the DeNovo assembly, I get this number and I am not sure about the meaning: 7223485 / 277277949 = 2.61% reads selected during normalization. 0 / 277277949 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 277277949 = 0.00% reads missing kmer coverage (N chars included?).
Does it mean that 2.61 % of the reads among all samples will be normalised and used to build the assembly?
When I run the read mapping of my samples back to the assembly made with them, the coverage is very low, ~25%.
Would you have any suggestion? and is that 2.61% as worrying as I think?
I am not an experienced bioinformatician, so I apologise if this question is silly.
Cheers, -Luca
