Using DESeq with Biological Replicates with Different RNAseq Read Lengths

[jbvt]

Is it okay to use DESeq with count data from biological replicates having different RNAseq read lengths?

thanks

[turnersd]

I might consider making this an element in your design table, as was done with the pasilla library type variable in the DESeq vignette. But I'm not sure how necessary. Perhaps others can share their thoughts.

[chadn737]

Does each replicate have different read lengths? If so, then I would certainly make this a factor.

[Wolfgang Huber]

To avoid biases by caused different efficiencies of the aligner in mapping reads with different length, one might shorten the longer reads to make them all have the same length.

Otherwise, I agree with Stephen and Chad(?). The ends will justify the means, and the usefulness of your result will depend on the relative sizes of the "batch effect" caused by your experimental design and the biological effect of interest.

Best wishes
Wolfgang