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?
0
gravatar for ASid
13 months ago by
ASid10
USA
ASid10 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 • 554 views
ADD COMMENTlink modified 5 weeks ago by Shicheng Guo8.0k • written 13 months ago by ASid10
3
gravatar for Rob
13 months ago by
Rob3.7k
United States
Rob3.7k 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 13 months ago by ATpoint29k • written 13 months ago by Rob3.7k
1
gravatar for swbarnes2
13 months ago by
swbarnes27.4k
United States
swbarnes27.4k 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 13 months ago by swbarnes27.4k
1
gravatar for genomax
13 months ago by
genomax78k
United States
genomax78k wrote:

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 COMMENTlink modified 13 months ago • written 13 months ago by genomax78k
0
gravatar for Shicheng Guo
5 weeks ago by
Shicheng Guo8.0k
Shicheng Guo8.0k wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Shicheng Guo8.0k
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