I had assembled a non-model system plant's RNA-seq reads by Trinity packages (without reference). After annotated the transcriptome by blast against model plant arabidopsis, I fount there was a specific gene (A) missed in the assembled transcriptome. Previous, other colleagues in the lab had checked the expression of A gene, and they did get some results.
In order to know why I couldn't get the A gene in the assembled transcriptome, I extracted the raw read sequences from FastQ file and blat against the published A-homologue sequence. There were only two reads could match with the homologue sequence, and there was a huge gap between them.
Have you ever meet such situation, and how to explain it? Does it mean the quality of that RNA-seq is not good enough? But I can get some other key genes, and their expression patterns were matched other RT-PCR results.
Many thanks,
CW
In order to know why I couldn't get the A gene in the assembled transcriptome, I extracted the raw read sequences from FastQ file and blat against the published A-homologue sequence. There were only two reads could match with the homologue sequence, and there was a huge gap between them.
Have you ever meet such situation, and how to explain it? Does it mean the quality of that RNA-seq is not good enough? But I can get some other key genes, and their expression patterns were matched other RT-PCR results.
Many thanks,
CW
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