Can I determine if RNA-SEQ data is forward stranded, reverse stranded, or unstranded from FASTQ file?

Question

[aaghodsinia]

Can I determine if RNA-SEQ data is forward stranded, reverse stranded, or unstranded from FASTQ file?

Answer 1

[ATpoint]

Not directly from the plain fastQ file, no. You will need to process it. The fastest way is probably to use Salmon with option -l A. This will make an automated guess about the strandedness. You can run a small subset of the entire fastQ to get the guess, maybe 500.000 reads or so. Be sure to also use the search function for related threads. This has been asked many! times before.