Import raw data from the Illumina platform

[Nicklas Nordborg]

A discussion about importing raw data from the Illumina platform was started on the mailing list. See:

​http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00500.html

Since it seems that the file format is not compatible with the existing import plugin a new plugin or something else is needed. One working solution (by Jeremy Davis-Turak) is to split the data file into one file for each hybridization with an R script and then use the regular import plugin.

Does anybody have any real and up-to-date Illumina files? We need some that we can do tests with. Without test data we are not able to create an integrated plug-in for the import.

[base]

R script to convert a multi-array Illumina .csv output file into multiple single-array files.

[base]

Extended properties file edited by Jeremy Davis-Turak to include reporter columns used by Illumina

[base]

Sample rat data.

[base]

Sample rat annotation file.

[base]

Sample human annotation file. Note the different number of columns per array (2) compared to the rat file, and the different number of arrays per chip (6, where rat has 12).

[base]

Example of a file resulting from the R script. Note that the column names are general.