Transcript data from "Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20"
This page includes downloads for viewing transcript data
from D. alaskensis G20, a table of potential transcript starts
(TSS), and R source code for inferring high-confidence TSS.
Viewing Transcript Data in Artemis
You can download a zip file here (37 MB).
You should start by opening the genbank file and then use
Graph / Add User Plot to add the art files, which including tiling data for rich and minimal media (richnorm3, minnorm3) and the 5' RNASeq data.
Potential Transcript Starts
See TSS_candidates.tab (tab-delimited file, 14,706 data rows).
Every local peak in the 5' RNASeq data with at least 50 reads and in a non-redundant part of the genome is included. The fields are:
- start, strand -- the location in the genome of the putative TSS
- nReads -- the number of 5' RNASeq reads
- bits.rpoD, bits.rpoN -- the bit score of the best hit to the respective motif, within 1 nt of the TSS
- loN, loBits, loTiling -- log odds for this to be a genuine TSS, given the number of reads, the motif bit scores, or the tiling data
- lo -- the log odds for this to be a genuine TSS. lo > 4 was considered high confidence.
R source code and image
- paper1.R -- source code in R for computing high-confidence TSS. (The table above corresponds to rpeaksG, although some column names were changed for clarity.)
- R image (80 MB)
Links to GEO
Page by Morgan Price, April 2014