Question: Is TCGA PRAD RNA-seq data strand specific?
gravatar for musaddeque.ahmed
3.3 years ago by
musaddeque.ahmed20 wrote:

I have been trying to find if TCGA PRAD (prostate cancer) RNA-seq data strand specific or not. I can not find any relevant info. I did find that it is Illumina protocol, but nothing more. Does anyone if they are strand specific? Do you have the right link? Thanks

prad strand rna-seq tcga • 1.8k views
ADD COMMENTlink modified 5 months ago by Zhenyu Zhang250 • written 3.3 years ago by musaddeque.ahmed20
gravatar for neethav
15 months ago by
neethav20 wrote:

All TCGA samples are non-stranded.

ADD COMMENTlink written 15 months ago by neethav20
gravatar for TriS
3.3 years ago by
United States, Buffalo
TriS3.9k wrote:

at the top of my head I don't know, however, there is a similar questions here on Biostar if you can find out the library preparation method/kit that might help.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by TriS3.9k
gravatar for Zhenyu Zhang
5 months ago by
Zhenyu Zhang250
United States
Zhenyu Zhang250 wrote:

The short answer is no.

The specific RNA-Seq library preparation kit TCGA used actually "could" support stranded library; however, it was used in a manner that libraries are actually strandless.

ADD COMMENTlink written 5 months ago by Zhenyu Zhang250
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