RNA-Seq:How to know RNA-seq data is Strand-Specific or not based on only fastq files available in public data repositories such as SRA?

Question

[ASid]

How To Find RNA-seq data is Strand-Specific or not based on only fastq files from information available in public databases. I am looking for information because I might not know if such information is also deposited in public repositories. Right now I am interested in knowing this information about SRA/GEO dataset GSE72086?

Answer 1

[Rob]

If you simply quantify the data with salmon using library type -l A, it will infer the most likely library format (stranded vs. unstranded) for you.

Answer 2

[swbarnes2]

If the library prep kit information is included, you can know from that. But it's probably easier to align and gauge strandedness empirically.

Answer 3

[GenoMax]

You will have to align the data (if the information about specificity can't be located). Then use infer_experiment.py included in RSeQC to find strandedness.

Answer 4

[Shicheng Guo]

the best way should be infer_experiment.py in RSeQC.

pip install RSeQC 
infer_experiment.py -r knowngene.hg19.bed12 -i Aligned.sortedByCoord.out.bam

knowngene.hg19.bed12 is downloaded from table browse in UCSC and an example like this and knowngene.hg19.bed12 can be downloaded here