Description
This track displays the probes from the Illumina WG-6 3.0 BeadChip.
The WG-6 BeadChip contains probes for the following set of RNA
transcripts:
| Probe source | Number of probes |
Number of unique probe sources |
| RefSeq NM (well-established coding transcript) | 27,454 |
22,435 |
| RefSeq XM (provisional coding transcript) | 7,870 |
7,518 |
| RefSeq NR (well-established non-coding transcript) | 446 |
358 |
| RefSeq XR (provisional non-coding transcript) | 196 |
190 |
| UniGene ESTs | 12,837 | 12,837 |
| TOTAL | 48,803 | 43,338 |
Display
The track shows the location of the probes on the genome after the RNAs
they correspond to were all aligned to the genome using BLAT. Alignment
scores range from 0 to 1000, where 1000 is a perfect score. In the
display, darker browns are for higher-scoring alignments.
Click on a probe track item to see detailed information about that probe ID.
View the base-by-base alignment for that probe by clicking the
"View Alignment" link on the details page.
Methods
The probe set was collected from the NCBI
GEO
(Gene Expression Omnibus), and the
43,338 RNA sequences were collected from Genbank using NCBI's EUtils interface
to Entrez. These RNAs were aligned to the genome using BLAT, and 43,224 of them
aligned well to 46,432 locations on the genome. The single best alignment was
used, except in 1,789 cases where the RNA mapped equally well to two or more
locations. The probes were then aligned to their respective RNAs using BLAT,
and if a good alignment resulted, the probe was then mapped through to the
genome using the combination of the probe-on-RNA and the RNA-on-genome
alignments. Of the 48,803 original probes, 40,852 map well
through this procedure to 44,163 locations on the genome.
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