|Citation||Graveley, B. (2011.1.5). modENCODE RNA-Seq junction data (Export to RIS)|
|Publication Type||Personal communication to FlyBase|
|Text of Personal Communication||
For the junctions, I've attached a file called
Cleanup_Junctions_w_counts.txt.bz2 which contains a list of 67,317
junctions from the Illumina RNA-Seq data that we analyzed in the paper.
The differences in numbers of junctions depend on what set you are
talking about and are represented by different subsets of junctions as
depicted in the Venn diagram in Supplementary Figure 9a of the Graveley
et al paper. The junctions you want to display are the 67,317
junctions from the Illumina only set, and match the number of junctions
plotted in the Venn diagram.
The first four columns in the file I've attached are Junction_ID
(format: chr_start_stop), chromosome, start, stop, followed by a read
count and entropy score column for each sample. In my opinion, it would
be best to provide both numbers. The read counts are simply the number
of reads observed that map uniquely to that junction, while the entropy
score is a confidence score in how "real" the junction is. You can have
junctions with high read counts but low entropy scores, and vice versa,
so both numbers are informative.
The samples are labeled in the table using BS numbers which have the
Brenton R Graveley
UConn Health Center
|Research paper||The developmental transcriptome of Drosophila melanogaster.
Graveley et al., 2011, Nature 471(7339): 473--479 [FBrf0213330]
|Personal communication to FlyBase||Total entropy scores for the 67,317 modENCODE junctions.
Graveley, 2011.11.3, Total entropy scores for the 67,317 modENCODE junctions. [FBrf0216691]
Additional low confidence modENCODE junctions.
Graveley, 2011.11.3, Additional low confidence modENCODE junctions. [FBrf0217580]
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|Associated Files||File date: 2011.1.5 ; File size: 26691069 ; File format: txt ; File name: Graveley.2011.1.5-Cleanup_Junctions_w_counts.txt|
|Language of Publication||English|
|Additional Languages of Abstract|
|Also Published As|
|Data from Reference|