Question: expression of transgenes
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gravatar for abryants
2.5 years ago by
abryants0
abryants0 wrote:

I work with Drosophila transcriptome and sometimes I need to evaluate expression of artificial transgenes, like LacZ, that are not part of the genome assembly. How can I do that? First, I thought of adding the LacZ sequence (as a separate contig) to the Drosophila genome assembly, but that would mean re-running the whole RNA-seq pipeline. What would be the most convenient and simple way to get only the transgene expression?

rna-seq • 594 views
ADD COMMENTlink written 2.5 years ago by abryants0

I guess at some point you are going to need to map reads to to a sequence. So I guess you can make an appropriately formatted fasta file and call it up from your history (most tools have this as an option for reference sequence). If you wanted to save time maybe you could only map reads which had failed to map to the genome ref sequence when if you did that already, I think this is quite easy if you use bowtie2. Cheers Guy

ADD REPLYlink written 2.5 years ago by Guy Reeves1.0k

This gives me some ideas. Appreciated!

ADD REPLYlink written 2.5 years ago by abryants0
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