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Reference Report
| Reference | |||
|---|---|---|---|
| Citation | Graveley, B. (2011.1.5). modENCODE RNA-Seq junction data (Export to RIS) | ||
| FlyBase ID | FBrf0212682 | ||
| Publication Type | Personal communication to FlyBase | ||
| PubMed ID | |||
| PubMed Abstract | |||
| 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 following translations: BS40 embryos0-2hr BS43 embryos2-4hr BS46 embryos4-6hr BS49 embryos6-8hr BS54 embryos8-10hr BS55 embryos10-12hr BS58 embryos12-14hr BS62 embryos14-16hr BS66 embryos16-18hr BS67 embryos18-20hr BS71 embryos20-22hr BS73 embryos22-24hr BS107 L1larvae BS111 L2larvae BS113 L3larvae_12hr_post_molt BS196 L3larvaePS_1-2 BS200 L3larvaePS_3-6 BS203 L3larvaePS_7-9 BS129 white_prepupae BS133 WPP_12hr BS136 WPP_24hr BS137 pupae_WPP_2d BS140 pupae_WPP_3d BS143 pupae_WPP_4d BS150 adult_male_1d BS156 adult_male_5d BS162 adult_male_30d BS153 adult_female_1d BS159 adult_female_5d BS165 adult_female_30d Cheers, Brenton R Graveley UConn Health Center |
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| DOI | |||
| Related Publication(s) | |||
| Research paper | The developmental transcriptome of Drosophila melanogaster. Graveley et al., 2011, Nature 471(7339): 473--479 [FBrf0213330] |
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| 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 Information
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| Comments | |||
| Associated Files | File date: 2011.1.5 ; File size: 26691069 ; File format: txt ; File name: Graveley.2011.1.5-Cleanup_Junctions_w_counts.txt | ||
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Other Information
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| Secondary IDs | FBrf0212803 | ||
| Language of Publication | English | ||
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Data from Reference
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