Hi, all:
when I checked my paired-end RNAseq data, I saw some weird result. Figure is here
basically two genome features have same coordinate(as highlighted in red), however, their fpkm value is different. I wonder anyone have some ideas why this occur?
By the way, I am using Tophat v2.0.4, Cufflinks v2.0.2 and cummeRbund v2.0.0.
Thanks.
Best, Liye
2 answers
Well the genes that you list there are not supposed to have the same coordinates ... so this means there is some inconsistency there - one or more of the files is not what you think they are - or something else ...
I check the annotation for DDX11L1 of chr1, which spans 11869 to 13670. And RP11-34P13.3 spans 29554 to 30039. And Has-mir-1302-2 starts from 30366 to 30503.
Therefore, I think the locus represents a transcript contig defined by cufflinks, which may include multiple transcripts. And each can have an unique ID. Therefore, both XLOC0001 and XLOC_00002 is within contig chr1:11868-31109. Therefore, it is possible that two transcripts within a contig have differential gene expression.
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