TODO.md

General pipeline

• normalized using median of gene expression ratio, same idea than DESeq2, for viz purpose

• add length enrichment function

• implement bayes function to decide which sequences go where

• sequence in the cluster - text

• create modules to save sqlite3 results

• add doc about web servers with downstream analysis: ** http://compbio.uthsc.edu/miR2GO/home.php

• create small stats: # of sequences, # in seqs.ma, # in alignment, # in clusters

• counts of aligned reads

• load matrix ma after alignment parsed

• NOW html to connect to sqlite3 db to viz results

• implement tRNA-scan

• NOW implement small rna prediction: CoRaL is an option for everything http://wanglab.pcbi.upenn.edu/coral/ or

• change to python alignment tool

• [-] implement mirna prediction http://evryrna.ibisc.univ-evry.fr/miRBoost/index.html (move inside bcbio)

• implement submire target prediction module http://research.nhgri.nih.gov/software/SubmiRine/user_guide.shtml

• Add to report: https://github.com/pkerpedjiev/forna/

modules

• QC:
  • figures 5' positions by # unique sequences, this by class: mirna, trna ...
• report:
  • add (R file) mirna path enrichment to report
  • limit number of sequences in html, like 1000 top

miraligner

Future implementation at http://mirtop.github.io

inputs will be fastq or bam file. Will need to download the mirbase annotation (and hairpin.fa) if not given (need version). Species is required (for now).

• create data set to test module
• align with razer3 if option on
• fix alignement error: get correct positions and guess additions
• decide best hits
• compare to mirbase ref: t5 t3 add mism
• ouput in SAM/BAM with custom flag for isomiRs
• make it compatible with old miraligner output and isomiRs

downstream

• isomirViz: html code to browse miraligner results for a project: preparation with miraligner module
• seqclusteR: will be an object that make easier to retrieve information like counts, rownames, annotations ... tidy tables, and figures

documentation

• add install subcommand for mirbase installation/genomes
• add html report link to documentation
• figure showing general pipeline steps: bcbio-nextgen
• add documentation for seqclusterViz html reader