Hello,
I am trying to decide what the best approach for running TopHat2 is. We have multiple RNA-Seq samples for two different conditions. Is it preferable to run TopHat2 for each individual sample, for all samples in each condition (2 runs only) or for all samples together? Does it make any difference in terms of the results? Running the software for each sample would be much faster, and seems preferable, unless there is a rationale for pulling the samples together (e.g. some of the junctions might be missed when individual samples are used).
Thank you!
Alexandra
I am trying to decide what the best approach for running TopHat2 is. We have multiple RNA-Seq samples for two different conditions. Is it preferable to run TopHat2 for each individual sample, for all samples in each condition (2 runs only) or for all samples together? Does it make any difference in terms of the results? Running the software for each sample would be much faster, and seems preferable, unless there is a rationale for pulling the samples together (e.g. some of the junctions might be missed when individual samples are used).
Thank you!
Alexandra
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