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Compare SE sequence with PE sequnce?
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13 months ago
star • 150
Netherlands

I have a RNA-seq samples that are SE with 50 bp and I would like to do DGE comparison with another set of RNA-seq data that are PE with the length of 100 bp. I would like to know is there any noticeable problem, comparing SE sequence with PE sequence?

RNA-Seq R • 348 views
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Were the different sample sets from different labs or even from the same lab but taken at different times/conditions? If so, I would be extremely wary of batch effects, which often have a very strong influence over RNA-seq data.

In terms of differences purely between 50 bp SE vs 100 bp PE, the latter will give give you a higher proportion of confidently correctly mapped reads. This will be especially true for repetative regions, which will be comparatively underrepresented or inaccurately quantified in the SE samples.

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If you include the type of sequencing (e.g. SE or PE) as a single covariate in your design model, then you should not have major issues. Obviously, it is better to have a good experimental design from the very start.

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As I understand it, the OP is trying to compare expression in one set of samples done with SE with that of another set done with PE, so adding SE/PE as a covariate will make no difference. If that's not the case then yes, you're correct.

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You're correct - it is not 100% clear in the question.

star, is the experimental setup the following:

  • All SE versus All PE

...or is it:

  • Mixed SE/PE versus Mixed SE/PE

?

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@ Kevin Blighe: thanks a lot, no I would like compare All SE versus All PE, that the latter is from another study.

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@ dr_bantz: Thanks a lot. These two sets of samples are from two different experiences, SE data is from our lab and the PE data is from another study with someone else.

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