improvements rnaseq pipeline

[cokelaer]

Future

• Duplication statistics: high coverage or PCR duplicates ? Spread over the transcriptome or localized on a set of genes. How distributed at the gene scale ?
• Add a column with list of genes corresponding to each GO term enriched (as present for KEGG)
• lncRNA analysis
  https://www.tandfonline.com/doi/full/10.1080/15476286.2021.1899673
• CircRNA analysis
  https://www.sciencedirect.com/science/article/pii/S1672022921000292
• tRNA abundance/modifcation
  https://www.sciencedirect.com/science/article/pii/S1097276521000484?via%3Dihub
• Gene fusion detection
  https://genome.cshlp.org/content/31/3/448.short?rss=1
• WGCNA and meta analysis
  https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1008976&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+ploscompbiol%2FNewArticles+%28PLOS+Computational+Biology+-+New+Articles%29
• Include String ?
  https://string-db.org/

oct 2021

• use new sequana-wrappers

Those requested features are for the rnadiff analysis, not sequana_rnaseq:

• if possible, provide resuls w/wo independent filtering
• we using --force (rnadiff), we should suppress previous DGE results otherwise they will be added to the HTML reports
• design add column 'alias name'

April/May/June 2021

• if pvalue == 0, should set a value so that it can be seen in volcano plot
• fastp tool to complement existing cutadapt trimming tool
• add html entry point for the enrichment (if several comparisons) or several enrichments
• refactorise sequana enrichment maybe to have syntax such as sequana enrichment panther"

march 2021

• better filtering for multiqc
• main summary.html should have more features/summary/plots
• check rnaseqc gtf input [catch missing GTF in the main.py and rnaseq.rules]. added a converter in sequana
  • gtf input (from GFF) for the prokaryotes case
  • gtf input (from GFF) for the eukaryotes case
• salmon for eukaryotes tested on mm10
• check rnaseqc multiqc module . no need for the biomics fork anymore.

Jan 2021

• BUG fix switch mark duplicates correctly for the qc and others
• Better GFF handling with custom gff able to handle several feature types, sanity checks of user's choice on attribute and feature
• Checked rna_sqc functionality and provide a gff2gtf parser in sequana.

Dec 2020

• Fix issue of seg fault for bacterial genomes with star aligner
• fastq_screen should work now. The only contaminants looked for is the phix. Other genome should be handled by the users (meaning build the indexing); fastq_screen searches for phix is now the default behaviour since the code should work out of the box
• fix missing workflow image in the report.
• add strandness plot in ./outputs directory and add the image in the summary plot
• bowtie1/star/bowtie2 indexing are now stored in their own sub-directories
• provide way to disable rRNA search
• fix issue related to star index rule bug in sequana
• rnadiff option is now set automatically to one_factor
• add option --run to execute the pipeline without manual checking (batch mode)

Oct-Nov 2020

• star index we may have warning.
  --genomeSAindexNbases 14 is too large for the genome size=4456448,
  which may cause seg-fault at the mapping step. Re-run genome generation with
  recommended --genomeSAindexNbases 10
• a more generic title in the multiqc_config

Sept 2020

• Add tolerance for feature_counts in the pipeline and config file after fixing sequana featurecounts functions (v0.9.17)

Aug 2020

• do_indexing option is now pre-filled when instanciating the pipeline.
• salmon option validateMappings is deprecated. to remove
• salmon indexing included
• refactorise the way feature counts are handled. Not in the onsuccess but a simpler code from @khourhin now included in sequana and this pipeline as of version 0.9.16 .

June/july 2020

• Fix R1/R2 issue for rRNA
• add mark duplicates in cluster config and set to False by default
• add paired option for feature counts when paired data is provided.
• add option to skip the fastqc on the raw data. This will be the default; The fastqc on the filtered data is kept by default.
• cleanup the multiqc option to exclude fastqc_samples (to not clash with fastqc_filtered)

April-May 2020

• if input genome size is >4billions Gb, the bowtie2 output extension are .bt2l (not .bt2) therefore, the sequana rule bowtie2_mapping should be updated and this pipeline as well.
• add input to the rnadiff analysis in ./rnadiff
• a faster --help option
• a --from-project option to import existing pipeline
• a HTML custom front page
• add feature counts as a single file

Jan 2020 - April 2020

• integrate the biomix scripts to make the link with the differential analysis
• add feature counts in separate directory ready to use by rnadiff
• integrate salmon

Dec 2019 - Jan 2020

• fix the RNAseQC rule, which is brojen at the moment
• check for rRNA feature name presence in the GFF
• check for feature count type provide by the user
• check config with schema
• fix read tag
• possiblity to switch off cutadapt
• fixing the bowtie2 config/pipeline conflict name (see explanation of the naming convention in the config and pipeline when using bowtie2_mapping rule #3)
• Fixing indexing issue: indexing is done even though not asked for or vice versa: when we set indexing to False, the pipeline fails with crypting message. We will provide a better handling of checking whether or not indexing is done.
• include the schema file
• parameter output-directory should be renamed output_directory in the multiqc section
• handle the stdout correctly inb the fastqc rule, bowtie2, bowtie1
• allow rRNA feature and/or files with meaningful error message if the 2 options conflict
• better multiconfig report (text/title)