Is it possible to compare gene expressions of two types of sequencing data, i.e. treated samples that are paired-end 50bp and untreated samples that are single-end 40bp? My idea is to get read counts from HTSeq-count, followed by DESeq2. HTSeq-count counts paired-end data as read pairs, therefore an aligned paired-end reads will only be counted as one. Because of this, I think I can do DE with paired end vs single end data?
Thanks! Jenn
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Jennifer •
1 answer
The paired-end reads should be counted only ones as one fragment.
You can include the library type in the design formula in DESeq2/edgeR. Something like design <- model.matrix(~libType+treat) in DESeq2
Otherwise, you can also use RUVSeq or other tools to remove any "batch" effects because of the lib type.
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