Insert Length Vs Nominal Length For Paired-End Data

Question

[Daniel Standage]

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?

Answer 1

[lh3]

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.

Answer 2

[Fabian Bull]

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.

Answer 3

[devbt15]

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.