Hello everybody,
we have to run some RNA-seq experiments on HiSeq 2500, and the sequencing facility has lots of experience with exomes/genomes resequencing, but very little experience with mRNA-seq. Overall, from what I know, the consensus is that for read count-based methods (ChIP-seq, RNA-seq) you want to run single-end sequencing with shorter read length, to get more individual reads from the same reagents.
What are the pitfalls and recommendations to get the best throughput from a single-end experiment in terms of cluster density, concentrations, etc?
Thank you in advance
we have to run some RNA-seq experiments on HiSeq 2500, and the sequencing facility has lots of experience with exomes/genomes resequencing, but very little experience with mRNA-seq. Overall, from what I know, the consensus is that for read count-based methods (ChIP-seq, RNA-seq) you want to run single-end sequencing with shorter read length, to get more individual reads from the same reagents.
What are the pitfalls and recommendations to get the best throughput from a single-end experiment in terms of cluster density, concentrations, etc?
Thank you in advance
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