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Old 07-07-2016, 06:51 AM   #1
ronaldrcutler
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Location: Virginia

Join Date: May 2016
Posts: 80
Default Gene Name nomenclature

Hello all. I have a set of DE genes from a single replicate as identified by the GFOLD package. Though I am getting results which have the same gene ID but different suffixes at the end of the name and different GFOLD levels. I used a .bed file for the annotation. Usually I use a .gff3 file with HTSeq-count.


It looks like this:

Code:
#GeneSymbol	                                                             GeneName  GFOLD(0.005)
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1	 NA	-4.50996
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds1	 NA	-3.62531
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds2	 NA	-2.81447
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds3	 NA	-3.38619
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds4	 NA	-2.05015
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds5	 NA	-1.9145
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds6	 NA	-2.44262
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds7	 NA	-3.6937
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds8	 NA	-1.33762
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds9	 NA	-3.64182
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.exon1 NA	-3.62531
Can anybody clarify to me the differences between these Gene Symbols? I am used to Gene names looking something like this:

Code:
42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+__chr9_10L
42SP50|c.XenBase_133737005|JGIv7b.000220448_3999398-4005758+__chr6L
A1CF|c.Taira201203intestine_X005935|JGIv7b.000079772_4581973-4609884+__chr7L
Thanks
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deseq, gfold, hisat2, rna-seq, tophat

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