Is the number of spots in SRA equal to the number of reads
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16 months ago
FadyNabil ▴ 10

I want to know if the number of spots in SRA equal to the number of reads or not

fasta SRA fastaq. • 549 views
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Someone has an old copy of SRA Handbook (from 2014) available which contains this gem:

A spot is a new kind of abstraction that captures all the data associated with one intensity function in time. Thus reads related by mate pairing or bar coding can be tracked implicitly by virtue of sharing a “reaction container.” The concept is roughly analogous to that of a growth template in capillary-based sequencing, in which mate pair reads are related by their sharing of an insert in the cloning vector.A read is classified as to whether it is a technical read (primer, linker, adapter, bar code, etc) or an application read (single read, paired ends, etc). Reads are indexed by one of three methods: base-based coordinates, cycle-based coordinates, or by alignment to an expected oligo sequence (such as a linker or bar code).Specification of spot decoding is done at the level of the experiment design, so that this information is bound once per experiment, and not once per read, as is currently done.

Does not make complete sense to me but this seems to be only used internally in SRA. This information is nowhere to be found in current documentation.

As always you should email SRA helpdesk and ask for an authoratitative response. Post their answer here.

Entering edit mode
16 months ago
Dunois ★ 2.0k

This discussion might be helpful to you: What Is A "Spot" In Sra Format.


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