The Wedring pipeline gathers some bioinformatic softwares to achieve differentially expressed genes from RNA-Seq experiments. It is implemented as a Python package, named wedring, and also has the command line interface wedr.

The softwares used are: Bowtie, TopHat, SAMtools, BEDTools and DESeq.

The pipeline has four stages:

• Pre-processing stage:

  The annotation file (in GFF format) is validated, according to its field numbers and new-line character.

• Indexing stage:

  The Burrows-Wheeler (BW) index is created from a reference genome using the bowtie-build program. This stage is optional since a prebuilt index may be provided to the pipeline.

• Mapping stage:

  RNA-Seq reads from different experimental conditions are mapped against the BW index. The mapping program may be Bowtie or TopHat, according to the user needing. Bowtie is recommended to analyze prokaryotic data. Meanwhile, TopHat is recommended to eukaryotic data due to the splicing junctions routines in its pipeline. Afterwards, informations from the mappings are processed using SAMtools and BEDTools to generate a counting table of each genomic features in each experimental condition.

• Differential expression stage:

  The counting table is used as the input to the DESeq pipeline. The result will be a table containing statistics of each genomic feature which includes p and fold change values.