miARmaSeq : miRNA And RNA Multiprocess Analysis.

Rocio Nuñez Torres, Eduardo Andrés-León & Ana M. Rojas.

It is a miRNASeq analysis workflow, which automatically performs several analysis processes using state-of-art software. It includes:


(a) Quality analysis of the reads (by FASTQ )
(b) Adapter removal using Cutadapt or Reaper software. If the adapter information is not available a computational prediction of the adapter sequence can be performed using Minion.
(c) Alignment to the reference genome (indexing is included within the pipeline) (by Bowtie1/2)
(d) Read quantification by desired feature (premiRNA, mature miRNA,...) using Htseq-Count.
(e) Quality analysis to determine the correlation among replicates using graphical approaches, such as PCA, MDS or hierarchical clustering
(f) Differential Expression Analysis (DEA) using EdgeR and/or NOISeq.

Our pipeline process standard sequencing files (fastq format) performing several and parallelized analysis resulting in a results file (in tsv format) with DEA features for each experimental condition evaluated and an additional quality report file. 

 More information at : http://miARmaSeq.cbbio.es


The DDR site: a Database of Human DNA Damage Response Proteins.

Eduardo Andrés-León, Ildefonso Cases & Ana M. Rojas.

This site as been developed to explore the data from our publication about the Emergence and Evolution of DDR proteins (published in MBE). It includes:

(a) Different searching modes, from text to fasta sequences
(b) Emergence data for proteins
(c) Alignments retrieval
(d) Phylogenetic analyses for DDR proteins
(e) Post-translational modifications
(f) All the data presented with links to literature


 

Explore the site and give us feedback: http://www.cbbio.es


 

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