Hello all!
This is my first post here! But I am not just new at the forum, I am also new on the field of RNA-seq. So please be lenient with me! (-; I already read a lot in this nice forum and many things gets clearer to me now. But at the moment I still have a question. I am sure somebody can answer…
We want to perform a whole transcriptome sequencing experiment using the Illumina HiScanSQ system. Samples will be obtained from fish and tapeworms. For the fish species an annotated reference genome is available. At the moment collogues are working on a reference genome for the tapeworm but I am not sure if it will be annotated till we need it.
We are now at a point where we have to decide for the library prep procedure. We want to isolate total RNA and analyze only mRNA – that is clear. What we are not sure about is whether we should perform directional (strand-specific) or non-directional sequencing.
I already tried to find out the advantages and disadvantages of both methods but I did not get satisfying answers. Could please somebody explain me the benefits of both methods and how the methods differ concerning data evaluation.
Thanks a lot!!!
Cheers
frefra
This is my first post here! But I am not just new at the forum, I am also new on the field of RNA-seq. So please be lenient with me! (-; I already read a lot in this nice forum and many things gets clearer to me now. But at the moment I still have a question. I am sure somebody can answer…
We want to perform a whole transcriptome sequencing experiment using the Illumina HiScanSQ system. Samples will be obtained from fish and tapeworms. For the fish species an annotated reference genome is available. At the moment collogues are working on a reference genome for the tapeworm but I am not sure if it will be annotated till we need it.
We are now at a point where we have to decide for the library prep procedure. We want to isolate total RNA and analyze only mRNA – that is clear. What we are not sure about is whether we should perform directional (strand-specific) or non-directional sequencing.
I already tried to find out the advantages and disadvantages of both methods but I did not get satisfying answers. Could please somebody explain me the benefits of both methods and how the methods differ concerning data evaluation.
Thanks a lot!!!
Cheers
frefra
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