Question: Insert Length Vs Nominal Length For Paired-End Data
4
gravatar for Daniel Standage
7.8 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

When looking at paired-end data in the NCBI SRA, sometimes the insert length is not listed, but it seems that nominal length is always listed under the library information. Is nominal length the same thing as insert length?

sra paired • 6.3k views
ADD COMMENTlink modified 23 months ago by devbt1510 • written 7.8 years ago by Daniel Standage3.9k
4
gravatar for lh3
7.8 years ago by
lh331k
United States
lh331k wrote:

From DRA:

Nominal Length: Average distance between the paired reads in base pair. This length can be determined by measuring the size distribution of the DNA fragments used for constructing the library.

The definition is vague, but my understanding is this is intended to mean the approximate insert size estimated during the library construction. It is "nominal" because people frequently fill this field before mapping and in that case, we do not really know the exact distribution.

I could be wrong. I do not work with SRA often.

ADD COMMENTlink modified 6.9 years ago by Istvan Albert ♦♦ 80k • written 7.8 years ago by lh331k
1
gravatar for Fabian Bull
7.8 years ago by
Fabian Bull1.3k
German
Fabian Bull1.3k wrote:

Typically the insert-size is the number of base-pairs between the paired-end reads. The nominal length is the distance between the two starting-nucleotides.

These therms are often mixed-up but they are different.

ADD COMMENTlink written 7.8 years ago by Fabian Bull1.3k
0
gravatar for devbt15
23 months ago by
devbt1510
devbt1510 wrote:

This page says that insert size is similar to nominal length: https://www.ebi.ac.uk/fg/annotare/help/seq_lib_spec.html Also the definition of nominal length on DDBJ Sequence Read Archive Handbook website (http://trace.ddbj.nig.ac.jp/dra/submission_e.html):

Nominal Length*: Size of the insert for Paired reads.

Hope it helps. D Das.

ADD COMMENTlink modified 23 months ago • written 23 months ago by devbt1510
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