Opened 16 years ago

Last modified 15 years ago

#486 closed task

Import raw data from the Illumina platform — at Version 5

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://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.

Change History (12)

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)

comment:4 Changed 15 years ago by Nicklas Nordborg

Description: modified (diff)

Changed 15 years ago by base

Attachment: gene_profile_Rat_sample.csv added

Changed 15 years ago by base

Sample rat data.

Changed 15 years ago by base

Sample rat annotation file.

Changed 15 years ago by 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).

Changed 15 years ago by base

Attachment: 1401771138_A.sample.txt added

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

comment:5 Changed 15 years ago by Nicklas Nordborg

Description: modified (diff)
Note: See TracTickets for help on using tickets.