Question: Alignment percentage for De novo analysis
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gravatar for madhul27_sit
6 months ago by
madhul27_sit0 wrote:

Hi, I have a data of silkworm (some rare species) whose genome is not reported yet. Thus I am doing De novo RNA seq analysis of it. I have followed Trinity protocol and when I perform RSEM for abundance estimation, it is giving me 50, 46, 51, 44 , 47 and 57 percent overall alignment rate, respectively, for each sample. Ideally, above 70% overall alignment rate is considered best. So, Does that mean there is a problem with data or should I try some other method for alignment and abundance estimation?

I have two samples with 3 biological replicates each.

rna-seq alignment assembly • 145 views
ADD COMMENTlink written 6 months ago by madhul27_sit0

By "followed the Trinity protocol", you mean you assembled the transcriptome with all the reads, then mapped each sample onto this reference transcriptome? What were the commands you used?

ADD REPLYlink written 6 months ago by h.mon23k
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