Kc167 whole cell CIP-TAP 876_879 smallRNA RNA-seq alignment and analysis (Celniker project, Gingeras subgroup)


Libraries were created from small RNA (less than 200nt) isolated from D. melanogaster Kc167 Nuclear CIP-TAP treated cell line extracts, sequenced using Illumina GAIIx with single-end modules, and aligned with NexAlign. Tracks show genomic features (exons or contigs), along with their rpkm, annotated from either dmel 5.32 or ginormous
Total read count: 57749413
Mapped read count: 23869488
Alignment rate: 41%

General Description

The cap-enriched and 5' monophosphate D. melanogaster small RNA libraries were generated in biological duplicate. Each library was mapped independently using STAR (Gingeras Lab) to the dm3 assembly without U-extra. To further assess the data we constructed contigs from the merged biological replciates and calculated Reads per Million values for every exon annotated in Flybase 5.32 and Ginormous. Additionally, we assessed each element for reproducibility using a nonparametric irreproducible detection rate script (npIDR, Alex Dobin Gingeras lab).


  1. Other Protocols: STAR sequence analysis, Analysis of smallRNA expression

Sample Details

  1. Animals/Lines: Drosophila melanogaster
  2. External Links: SRR350849, SRR350854

Related modENCODE submissions:

Release Date: 2012-01-25