Opened 18 years ago
Last modified 17 years ago
#486 closed task
Import raw data from the Illumina platform — at Version 5
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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| Priority: | minor | Milestone: | BASE 2.4 |
| Component: | coreplugins | Version: | |
| Keywords: | Cc: |
Description (last modified by )
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 by , 18 years ago
| Milestone: | → BASE 2.x+ |
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by , 18 years ago
| Attachment: | Illumina conversion.txt added |
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by , 18 years ago
| Attachment: | extended-properties.xml added |
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Extended properties file edited by Jeremy Davis-Turak to include reporter columns used by Illumina
comment:2 by , 17 years ago
| Milestone: | BASE 2.x+ → BASE 2.4 |
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comment:3 by , 17 years ago
| Description: | modified (diff) |
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comment:4 by , 17 years ago
| Description: | modified (diff) |
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by , 17 years ago
| Attachment: | gene_profile_Rat_sample.csv added |
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by , 17 years ago
| Attachment: | gene_profile_human_sample.csv added |
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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).
by , 17 years ago
| Attachment: | 1401771138_A.sample.txt added |
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Example of a file resulting from the R script. Note that the column names are general.
comment:5 by , 17 years ago
| Description: | modified (diff) |
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R script to convert a multi-array Illumina .csv output file into multiple single-array files.