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| data:olink [2026/01/19 16:23] – Create page to describe how the counts are made in 2026 Richard Bowers | data:olink [2026/01/20 11:51] (current) – Library type no longer has hyphen Richard Bowers |
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| ====== Olink Sequencing Counts ====== | ====== Olink Sequencing Counts ====== |
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| We support Olink sequencing and have included running ''ngs2counts'' in our sequencing pipeline to produce the counts for all lanes that have the library type "''O-link''". These counts are performed across one or more lanes on the flowcell, which is unusual for our service where everything else is supplied on a lane by lane basis. | We support Olink sequencing and have included running ''ngs2counts'' in our sequencing pipeline to produce the counts for all lanes that have the library type "''Olink''". These counts are performed across one or more lanes on the flowcell, which is unusual for our service where everything else is supplied on a lane by lane basis. |
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| ===== Counting ===== | ===== Counting ===== |
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| To produce the counts our pipeline selects the lanes that contain Olink data and groups them by SLX identifier. ''ngs2counts'' is then run **per SLX pool** across the lane or lanes that contain that pool. The result is a //zip// archive containing the results of the count and the ''run_metadata.json'' file. The file is named to include all the lanes from the run that it has included in the count, following the pattern: | To produce the counts our pipeline selects the lanes that contain Olink data and groups them by SLX identifier. ''ngs2counts'' is then run **per SLX pool** across the lane or lanes that contain that pool. The result is a //zip// archive containing the results of the count and the ''run_metadata.json'' file. The file is named to be attached to the minimum lane number for each SLX pool, though it will have the counts for all lanes for the same pool. It will be named: |
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| <code> | <code> |
| <SLX>.<FLOWCELL>.s_<LANES>.olink_counts.zip | <SLX>.<FLOWCELL>.s_<LANE>.olink_counts.zip |
| </code> | </code> |
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| <code> | <code> |
| SLX-0.233MNYLT4.s_257.olink_counts.zip | SLX-0.233MNYLT4.s_2.olink_counts.zip |
| <code> | </code> |
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| ===== Olink Library Numbering ===== | ===== Olink Library Numbering ===== |
