Opened 16 years ago

Last modified 15 years ago

#486 closed task

Import raw data from the Illumina platform — at Version 3

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.4
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by Nicklas Nordborg)

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

http://sourceforge.net/mailarchive/forum.php?thread_id=31600057&forum_id=12992

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.

Change History (5)

comment:1 Changed 16 years ago by Jari Häkkinen

Milestone: BASE 2.x+

Changed 16 years ago by base

Attachment: Illumina conversion.txt added

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

Changed 16 years ago by base

Attachment: extended-properties.xml added

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

comment:2 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.x+BASE 2.4

comment:3 Changed 15 years ago by Nicklas Nordborg

Description: modified (diff)
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