Question: Trinity DeNovo assembly and problems to map reads to it
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gravatar for luca.rugiu
9 weeks ago by
luca.rugiu0
luca.rugiu0 wrote:

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

trinity rna-seq assembly • 145 views
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