Assays

Short Name: 05_DE_limma-R Assay Class: DRY Assay Type: R Title: DE analysis for Illumina reads mapped to P citri IsoSeq transcriptome Description: Differential expression analysis for Illumina RNA-Seq reads mapped to P citri IsoSeq transcriptome pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Files connected to study: _S_P4_Pcitri_IsoSeq

Short Name: 01_NGI-IsoSeq Assay Class: WET Assay Type: IsoSeq Title: Raw data and SMRTLink analysis performed by NGI Sweden Description: Data downloaded from NGI Sweden with analysis leading to polished high-quality full-length Iso-Seq isoforms pISA Assay creation date: 2020-09-18 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: SRR15093694

Short Name: 02_cDNAcupcake-dry Assay Class: DRY Assay Type: dry Title: cDNA cupcake pipeline analysis of P. citri IsoSeq data Description: Pipeline with scripts for Iso-Seq after clustering step pISA Assay creation date: 2021-09-18 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 03-IPS Assay Class: DRY Assay Type: IPS Title: InterProScan for P citri unmapped transcripts Description: Prediction of ORF usning ANGEL (https://github.com/PacificBiosciences/ANGEL) and InterProScan Pfam domain search for all Iso-Seq isoforms that did not map to the P citri genome pISA Assay creation date: 2020-09-21 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: 04_mapIllumina-STAR Assay Class: DRY Assay Type: STAR Title: Mapping Illumina reads to P citri Iso-Seq transcriptome Description: Mapping and counting Illumina reads to P citri Iso-Seq transcriptome using STAR pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: