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docs: updated to ngs-template metadata fields
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Metadata field Definition Format Ontology Example | ||
assay_ID Identifier for the assay that is at least unique within the project <code_name\>_YYYYMMDD CHIP_20200101 | ||
assay_type The type of experiment performed, eg ATAC-seq or seqFISH ontology field- e.g. EFO or OBI ChIPseq | ||
assay_subtype More specific type or assay like bulk nascent RNAseq or single cell ATACseq ontology field- e.g. EFO or OBI bulk ChIPseq | ||
owner Owner of the assay (who made the experiment?). <First Name\> <Last Name\> Jose Romero | ||
platform The type of instrument used to perform the assay, eg Illumina HiSeq 4000 or Fluidigm C1 microfluidics platform ontology field- e.g. EFO or OBI Illumina | ||
extraction_method Technique used to extract the nucleic acid from the cell ontology field- e.g. EFO or OBI | ||
library_method Technique used to amplify a cDNA library ontology field- e.g. EFO or OBI | ||
external accessions Accession numbers from external resources to which assay or protocol information was submitted eg protocols.io, AE, GEO accession number, etc GSEXXXXX | ||
codename Internal code name for easy identification (like a keyword) Oct4_ChIP | ||
date Date of assay creation YYYYMMDD 20200101 | ||
nsamples Number of samples analyzed in this assay <integer\> 9 | ||
is_paired Paired fastq files or not <single OR paired\> single | ||
pipeline Pipeline used to process data and version nf-core/chipseq -r 1.0 | ||
strandedness The strandedness of the cDNA library <+ OR - OR *\> * | ||
processed_by Who processed the data <First Name\> <Last Name\> Sarah Lundregan | ||
organism Organism origin <Genus species\> Mus musculus | ||
origin If it is internal or external data <internal OR external\> internal | ||
path Path to files </path/to/file\> | ||
short_desc Short description of the assay plain text Oct4 ChIP after pERK activation | ||
labguru_ID ID of the experiment/assay in labguru_ID plain text | ||
Metadata field Definition Format Example | ||
assay_id Identifier for the assay <assay\>_<codename\>_YYYYMMDD CHIP_Oct4_20200101 | ||
assay What kind of NGS was used in your experiment? "[""CHIP"", ""RNA"", ""ATAC"", ""SCR"", ""PROT"", ""CAT"", ""CAR"", ""RIME"", ""TAP""]" ChIPseq | ||
owner Who performed the experiment? <First Name\> <Last Name\> Jose Romero | ||
date Date of sequencing, should be the same as defined by Genomics Platform in YYYYMMDD format! YYYYMMDD 20200101 | ||
codename Your name initials [Example: JB for Josh Brickman] <Initials OR keyword\> JR | ||
eln_id Optional: Electronic lab notebook ID Free text 12345 | ||
technology What technology was used? [Example: 10X Genomics if you used SCR] Free text 10X genomics | ||
sequencer What sequencing machine was used? [Example: NovaSeq 2000/NextSeq 2000/NextSeq 500] Free text NextSeq 2000 | ||
seq_kit What sequencing kit did you use? Please provide product number if available Free text | ||
n_samples How many samples have been sequenced? <integer\> 9 | ||
is_paired Paired fastq files or not <single-end OR paired-end\> single-end | ||
pipeline Pipeline name [Example: nf-core/rnaseq 3.12.0 or custom] Free text nf-core/chipseq -r 1.0 | ||
processed_by Person responsible for pre-processing (pipeline execution) <First Name\> <Last Name\> Sarah Lundregan | ||
organism What organism is this? <mouse OR human OR other\> mouse | ||
organism_version Which version of genome was used [Example: mm10, hg38] Free text mm10 | ||
organism_subgroup In vitro or in vivo? <in vivo OR in vitro\> in vitro | ||
origin Is this internal experiment of external (collaborator/publication)? <internal OR external\> internal | ||
note Optional: Was there something worth knowing? Free text Low quality experiment/Indexes are swapped ... | ||
genomics_path Path to where the data is </path/to/file\> smb:/path/to/file |
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Metadata field Definition Format Ontology Example | ||
project Project ID <surname\>_et_al_2023 proks_et_al_2023 | ||
author Owner of the project <First name\> <Surname\> Martin Proks | ||
date Date of creation YYYYMMDD 20230101 | ||
description Short description of the project Plain text This is a project describing the effect of Oct4 perturbation after pERK activation | ||
Metadata field Definition Format Example | ||
project Project name <name\>_<keyword\>_YYYY lundregan_oct4_2023 | ||
author Owner of the project <First name\> <Surname\> Sarah Lundregran | ||
date Date of creation YYYYMMDD 20230101 | ||
description Short description of the project Plain text This is a project describing the effect of Oct4 perturbation after pERK activation |