We had a RNA-seq experiment for a plant material (no genome reference available), 6 samples, 3Gb Illumina Hiseq PE reads for each sample. The transcriptome reference was constructed with Trinity and then the reads of each sample were aligned to this constructed reference with Bowtie2. The overall alignment rate is over 80%. But the reads count aligned to several housekeeping genes were extremely low, about 10-40 reads per gene. Is this result normal?
Question: Is it normal to have low expression levels of house keeping genes in plant RNA-seq results
22 months ago by
shuchen • 10
shuchen • 10 wrote:
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