TSS assembly pipeline for Sc_EPDnew_002
This document provides a technical description of the transcription
start site assembly pipeline that was used to generate EPDnew
version 002 for S. cerevisiae.
Apr 2011 R64/sacCer3
Assembly pipeline overview
Description of procedures and intermediate data files
1. Download annotated TSS
Data was downloaded from
UCSC table browser
Transcrips have been filtered according to the following rules:
- Transcripts of protein coding genes only
- Transcript lies on full chromosomes
- Genes must be annotated [Associated Gene Name present]
- Gene and transcripts status known
Gene names were taken from the field "Associated Gene Name". Since the
EPD format doesn't allow gene names longer than 18 characters,
we checked whether the names repsected this limitation.
A total number of 6692 promoters were selected.
2. SGD TSS collection
The SGD TSS collection is stored as a tab-deliminated text file
conforming to the SGA format under the name:
The six field contain the following kinds of information:
- NCBI/RefSeq chromosome id
- strand ("+" or "-")
- gene name
Note that the second and forth fields are invariant.
3. Import CAGE data
Data was imported from GEO as SRA file format. Raw sequence files were
mapped to sacCer3 genome using Bowtie. The resulting BAM files were converted to SGA file format using
A step-by-step guide on how to import, map and convert these samples can be found here
5. mRNA 5' tags peak calling
For each individual sample (19), peak calling for the merged file has been
carried out using ChIP-Peak
on-line tool with the following parameters:
- Window width = 200
- Vicinity range = 200
- Peak refine = Y
- Count cutoff = 9999999
- Threshold = 5
6. TSS validation and shifting
Each sample in the collection (mRNA peaks and SGD TSS) was then
separately processed in a pipeline aiming at validating transcription
start sites with mRNA peaks. A SGD TSS was experimentally confirmed
if an mRNA peak lied in a window of 500 bp around it. The validated
TSS was then shifted to the nearest base with the higher tag
7. SGD not-validated TSS
The total number (summing up all samples) of non experimentally validated TSS was around 3000.
8. Promoter collection for each sample
Each sample in the dataset was used to generate a separate
promoter collection. Potentially, the same transcript could be
validated by multiple samples and it could have different start
sites in different samples. To avoid redundancy, the individual
collections were used as input for an additional step in the
analysis (Assembly pipeline part B).
9. Merging collections and second TSS selection
The 3 promoter collections were merged into a unique file and
further analysed. Transcript
validated by multiple samples could potentially have the TSS set
on a broader region and not to single position. To avoid such
inconsistency, for each transcript we selected the position that
was validated by the larger number of samples as the true TSS.
Transcription Start Sites that mapped closed to other TSS that
belonged to the same gene (500 bp window) were merged into a
unique promoter following the same rule: the promoter that was
validated by the higher number of samples was kept.
10. Final EPDnew collection
The 4300 experimentally validated promoter were stored in the
EPDnew database that can be downloaded from our ftp
site. Scientist are wellcome to use our other tools ChIP-Seq
correlation analysis) and SSA
(for motifs analysis
around promoters) to analyse EPDnew database.