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Question: is it possible to use paired-end RNA-seq data? #13

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tomsing1 opened this issue Dec 9, 2023 · 1 comment
Open

Question: is it possible to use paired-end RNA-seq data? #13

tomsing1 opened this issue Dec 9, 2023 · 1 comment

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@tomsing1
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tomsing1 commented Dec 9, 2023

Context: I have paired-end RNA-seq data from a stranded library preparation protocol. I would like to identify differential splicing events between two groups (including cryptic exons). Is it possible / useful to use both the R1 and R2 reads in the analysis?
Many thanks for making SPLASH available - and congratulations on the Cell paper!
@roozbehdn
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Hi Thomas,
Sorry for our late response. Yes, you can run SPLASH on R1 fastq files and it should work for detecting differential splicing between two groups.

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@tomsing1 @roozbehdn