I would love some input on this one. I have collected samples from an exposure and my goal is to perform RNA Seq to investigate differential gene expression. As there is no reference genome for my species (Chironomid dilutus in case anyone is wondering) I will have to do a de novo assembly of the transcriptome. My plan is to use all reads from each sample (one sample per lane, 3 lanes) to assemble my transcriptome, and then perfrom expression analysis for each sample. What I need to decide upon is whether to go with Single End or Paired-End sequencing. I realize that the de novo assembly will be "easier" with paired-end reads, but I will lose depth of coverage with paired ends compared to single ends. So, is the de novo assembly that much more reliable with paired-end reads that it outweighs the loss of coverage?
I am rather new to this area so my question may be naive. I continue to read what I can but I find that forums such as this are much better resources than reading the primary literature.
I am rather new to this area so my question may be naive. I continue to read what I can but I find that forums such as this are much better resources than reading the primary literature.
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