TSS assembly pipeline for Sp_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. pombe.
Aug 2015 ASM294v2/spo2
Assembly pipeline overview
Description of procedures and intermediate data files
1. Download annotated TSS
Data was downloaded from
database the 02-02-2015.
Transcrips have been filtered for protein coding gene only, removing pseudogenes from the list.
Gene names were taken from the field "Locus ID". 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 5128 promoters were selected.
2. SGD TSS collection
The RefSeq 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 ArrayExpress as FASTQ file format. Raw sequence
files were mapped to spo2 genome using Bowtie (trimming 1bp from the
5-end). The resulting BAM files were converted to SGA file format
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 (3), 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 UCSC TSS) was then
separately processed in a pipeline aiming at validating transcription
start sites with mRNA peaks. A UCSC 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. UCSC not-validated TSS
The total number (summing up all samples) of non experimentally validated TSS was around 2000.
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 sample-specific promoter collections were merged into a unique
file and further analyzed. Transcripts validated by multiple samples
could potentially have the TSS set on a broader region
rather than a 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
experimentally validated promoters were stored in the
EPDnew database, which can be downloaded from our ftp
site. Scientists are welcome to use our other tools
(for correlation analysis) and
(for motif analysis around promoters) to analyze the