Hello SeqAnswers and thanks for your time.
I have a question about RNA-seq with sensitivity in mind. According to Genohub, 30+ M reads are suggested for transcript discovery in bacteria. However, Encode and Genohub both suggest 100-200M reads for the human transcriptome. For every megabasepair of the human transcriptome (conservative estimate of 140Mbp), between 0.71-1.43 million clusters should be sequenced (this ratio would decrease for a larger estimate of the transcriptome) to achieve suggested depth. For bacteria (with a considerably simpler transcriptome) with 4Mbp transcriptome, their suggestion (30-65M reads) yields a much larger ratio of 7.5-16.25M clusters/Mbp of transcriptome. In contrast, if ~12.5M clusters were sequenced per sample, the ratio would be closer to 3.125, still exceeding ENCODE best-practices for low-abundance/transcript discovery purposes.
TLDR:
For a bacteria with 4Mbp transcriptome, do you think is 12.5M clusters/sample sufficient for low-abundance transcript discovery?
I have a question about RNA-seq with sensitivity in mind. According to Genohub, 30+ M reads are suggested for transcript discovery in bacteria. However, Encode and Genohub both suggest 100-200M reads for the human transcriptome. For every megabasepair of the human transcriptome (conservative estimate of 140Mbp), between 0.71-1.43 million clusters should be sequenced (this ratio would decrease for a larger estimate of the transcriptome) to achieve suggested depth. For bacteria (with a considerably simpler transcriptome) with 4Mbp transcriptome, their suggestion (30-65M reads) yields a much larger ratio of 7.5-16.25M clusters/Mbp of transcriptome. In contrast, if ~12.5M clusters were sequenced per sample, the ratio would be closer to 3.125, still exceeding ENCODE best-practices for low-abundance/transcript discovery purposes.
TLDR:
For a bacteria with 4Mbp transcriptome, do you think is 12.5M clusters/sample sufficient for low-abundance transcript discovery?
Comment