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chr1:4847775-4887990W:NM_001159750:1:2668:917:1137:S/2

Unique IDs for paired reads

In order to support ids for paired reads, the Simulator Parameters support a UNIQUE_IDS options. If this option si senabled and paired reads are simulated, the inforamation about the relative orientation is not added to the read ids. This allows the simulator to create read ids for a set of paired reads that are unique except for the /1 /2 pair identifiers. Because it is a random process and does not effect the result, the simulator incorporates the information about the relative orientation into the /1, /2 pair identifier. If UNIQUE_IDS is enabled, all sense reads (S without UNIQUE_IDS) will be /1, and all anti-sense reads (A without UNIQUE_IDS) will be /2.

For example, here is a set of paired read ids without UNIQUE_IDS:

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chr1:4847775-4887990W:NM_001159750:1:2668:917:1137:A/1
chr1:4847775-4887990W:NM_001159750:1:2668:917:1137:S/2

With UNIQUE_IDS enabled, the same ids become:

Code Block
chr1:4847775-4887990W:NM_001159750:1:2668:917:1137/1
chr1:4847775-4887990W:NM_001159750:1:2668:917:1137/2
Note

With UNIQUE_IDS enabled, in the current Simulator (version 1.2.1) the reads produced carry a strand information, as by mate 1 always is sense (and mate 2 correspondingly anti-sense). See also a corresponding discussion in the forum.