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- Short read alignments data, aka "next generation sequence data" (BAM format)
- Standard annotations such as RefSeq annotations, provided by public repositories.
- Alignments of Affymetrix probe sets to the genome, provided by the NetAffx group at Affymetrix (link.psl format).
- Alignments of ESTs or mRNAs produced by blat (psl formats).
- Tiling array graphs, from the TAS program from Affymetrix.
- Copy number graphs from the CNAT program Affymetrix.
- Data generated from other Affymetrix software tools, such as GCOS, Expression Console and ExACT.
- Annotation and graph files prepared by any method in any of the supported formats.
The full A list of supported file formats is here.
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