Question: 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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gravatar for amnahsiddiqa
6 days ago by
Pakistan
amnahsiddiqa0 wrote:

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 • 101 views
ADD COMMENTlink modified 6 days ago by swbarnes24.7k • written 6 days ago by amnahsiddiqa0
1

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.

ADD REPLYlink modified 6 days ago • written 6 days ago by genomax60k
3
gravatar for Rob
6 days ago by
Rob2.9k
United States
Rob2.9k wrote:

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.

ADD COMMENTlink modified 5 days ago by ATpoint12k • written 6 days ago by Rob2.9k
1

This is probably the fastest method you'll find. Adding on this, once you quantified your data, you'll find in the specified output directory in the subfolder logs a log file in the specified output directory, which contains a line like:

[2019-01-04 11:18:39.780] [jointLog] [info] Automatically detected most likely library type as ISF

which tells you the inferred library type.

ADD REPLYlink written 5 days ago by ATpoint12k
1
gravatar for swbarnes2
6 days ago by
swbarnes24.7k
United States
swbarnes24.7k wrote:

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

ADD COMMENTlink written 6 days ago by swbarnes24.7k
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