Entering edit mode
2.9 years ago
bbyturner
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0
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?
Thanks! Yep, I have the fastq files. I've been using Kallisto, would I basically just read in only R1?
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.