gravatar for Sammy

3 hours ago by

United Kingdom


I just want to check my experiment design with you:

I was given RNA-SEQ samples from some genetically engineered bacteria. So those bacteria contain their basic genome and an insert (pET plasmid). Goal: quantify the expression of the plasmid.

What I've done:

  1. Bowtie2: aligned the reads to the reference genome; extracted unaligned genes.

  2. Trinity: created a transcriptome assembly using the unaligned reads (assuming they are the ones corresponding to the plasmid).

  3. Trinity: Align reads [Bowtie2] and estimate abundance where I'm feeding it the transcriptome assembly from step 2 and the RNA-SEQ data.

Does it make sense?


3 hours ago


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