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?
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2.9 years ago
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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?

rna-seq • 1.7k views
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Rob 5.0k

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.

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2.9 years ago

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

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GenoMax 110k

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.

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23 months ago
Shicheng Guo ★ 8.9k

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

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