Question: question about unstranded RNA-seq
1
gravatar for biolab
4.4 years ago by
biolab1.1k
biolab1.1k wrote:

Hi everyone,

I have an unstranded RNA-seq data.  I have a question about this seq type:

if several reads were mapped onto an intergenic region, it indicates presence of a noncoding RNA; however, which strand this ncRNA is derived from?  To my understanding, in the unstranded library construction method, both sense and antisense strands are produced before sequencing, so which strand the reads come from?

Any of your answers will be appreciated.  Thanks a lot!

 

rna-seq unstranded • 2.3k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 4.4 years ago by biolab1.1k
2
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

You can't determine which strand a feature is from with an unstranded kit.

ADD COMMENTlink written 4.4 years ago by Devon Ryan90k
1

Hi Devon,

I make an example as follows.  Suppose a read sequence is: 5' AAAAAGGGTTTTT 3'

The two strands are:

5' TTTAAAAAGGGTTTTTAAA 3' (+ strand)

3' AAATTTTTCCCAAAAATTT 5' (- strand)

So, this read must come from + strand.  I can determine the read origin. Am I right? Thanks.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by biolab1.1k
2

You can determine which strand a read maps to, but that does not reflect which strand coded for the RNA, and thus is not particularly useful.

ADD REPLYlink written 4.4 years ago by Brian Bushnell16k

Isn't the strand complementary to the RNA's sequence producing it?

ADD REPLYlink written 4.4 years ago by Parham1.4k
1

not in unstranded kit

ADD REPLYlink written 4.4 years ago by Nicolas Rosewick7.6k
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