Complete setup for ENA popup "pre filters"

[NoopDog]

Need

When launching the ENA pop-up we filter if possible by the filters required by the workflow (e.g. WGS, PAIRED or WGS SINGLE ). What is the complete set of workflow types, and what are the filters needed for each type? I think we have just a few types, so hopefully not much to "hard code' till we want to make this more flexible.

[NoopDog]

@mvdbeek, @d-callan, @nekrut, what are any other variable types we should add to the workflows.yml for the ENA picker?

We have

• SANGER_READ_RUN_PAIRED
• SANGER_READ_RUN_SINGLE

But ENA has other data types like the ones listed below for fun.... ;)

Should any of our workflows be set up to add any of these data types as default filters?
Is there any other interesting value to pre-filter on besides Library Layout and Strategy?

• WGS: Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)

• WGA: Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)

• WXS: Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)

• RNA-Seq: Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details)

• snRNA-seq: Single nucleus RNA sequencing is a method for profiling gene expression in cells which are difficult to isolate.

• ssRNA-seq: Strand-specific RNA sequencing.

• miRNA-Seq: Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details)

• ncRNA-Seq: Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or piRNA/piwi/RNA (piwi-interacting RNA).

• FL-cDNA: Full-length sequencing of cDNA templates

• EST: Single pass sequencing of cDNA templates

• Hi-C: Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing.

• ATAC-seq: Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA.

• WCS: Random sequencing of a whole chromosome or other replicon isolated from a genome.

• RAD-Seq: Restriction site associated DNA markers.

• CLONE: Genomic clone based (hierarchical) sequencing.

• POOLCLONE: Shotgun of pooled clones (usually BACs and Fosmids).

• AMPLICON: Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA.

• CLONEEND: Clone end (5’, 3’, or both) sequencing.

• FINISHING: Sequencing intended to finish (close) gaps in existing coverage.

• ChIP-Seq: ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein.

• MNase-Seq: Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached.

• Ribo-Seq: Ribosome profiling (also named ribosome footprinting) uses specialized messenger RNA (mRNA) sequencing to determine which mRNAs are being actively translated and produces a “global snapshot” of all the ribosomes active in a cell at a particular moment, known as a translatome.

• DNase-Hypersensitivity: Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.

• Bisulfite-Seq: MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.

• CTS: Concatenated Tag Sequencing

• ChM-Seq: ChIPmentation combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase (see pubmed 26280331 for details)

• GBS: Genotyping by sequencing is a method to discover single nucleotide polymorphisms for genotyping studies.

• MRE-Seq: Methylation-Sensitive Restriction Enzyme Sequencing.

• MeDIP-Seq: Methylated DNA Immunoprecipitation Sequencing.

• MBD-Seq: Methyl CpG Binding Domain Sequencing.

• NOMe-Seq: Nucleosome Occupancy and Methylome sequencing.

• Tn-Seq: Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets inserted into each gene of a colony after some time.

• VALIDATION: CGHub special request: Independent experiment to re-evaluate putative variants.

• FAIRE-seq: Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin.

• SELEX: Systematic Evolution of Ligands by Exponential enrichment

• RIP-Seq: Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP).

• ChIA-PET: Direct sequencing of proximity-ligated chromatin immunoprecipitates.

• Synthetic-Long-Read: binning and barcoding of large DNA fragments to facilitate assembly of the fragment

• Targeted-Capture: Enrichment of a targeted subset of loci.

• Tethered Chromatin Conformation Capture: Tethered Chromatin Conformation Capture.

• OTHER: Library strategy not listed.

[d-callan]

is this two tickets in one? or maybe im just not sure what were asking.. ill answer a couple possible questions and you let me know if i dont hit what you were after

on prefilters for current workflows:
there are workflow categories currently like 'variant calling' and 'transcription' and i suspect we could map these to library strategy pretty easily like transcription -> rna-seq for ex. not perfect, but something to get us started without hard coding that we can expand on meaningfully and modify as we go as needed? if you dont want to do that, and want to hard code for now, then id say if you arent filtering the two bulk rnaseq workflows on lib strategy = rna-seq then we should

on other data types:
i can see a number of those listed would already be interesting. whats stopping us from using any these now? it seems naively like if were filtering on these in the ui, we should be able to grab any to make a collection w? are the pre-filters tied to the variables you mention?
SANGER_READ_RUN_PAIRED
SANGER_READ_RUN_SINGLE

[d-callan]

is this ticket being open yet the reason why when i try to configure an rnaseq workflow it filters to 'WGS' for lib strategy? bc that needs fixing..