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Can I combine both single and paired end RNA-seq replicates for analysis?

I have some older samples that were processed with single end RNA-seq and newer replicates that was sequenced using paired-end instead. Is it possible to process these two datasets and analyze them together?

rna-seq sequencing
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updated by ATpoint ATpoint • written by bbyturner • bbyturner

1 answer

It would be better to simply treat the paired-end samples as single-end by only using R1 for alignment/quantification, that will eliminate the single/paired bias. Do you have the fastq files available?

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written by ATpoint ATpoint

Thanks! Yep, I have the fastq files. I've been using Kallisto, would I basically just read in only R1?

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written by bbyturner • bbyturner

Yes, that is what I'd do. Otherwise you create a mappability bias (paired-end may align "better" / differently than single-end), and as you cannot "upgrade" paired-end to single-end in silico you will need to stick to the "weakest link of the chain" which is "downgrading" the paired-end to single-end data by only using R1 as you say.

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written by ATpoint ATpoint

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