Assays

Short Name: 04_mapReadsToAs2-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly2 Description: STAR mapper was used to map back P citri RNAseq reads used for generation the de-novo assembly2. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 05_As2_tr_limmaDE-R Assay Class: DRY Assay Type: R Title: Assembly2 transcripts differential expression analysis using limma voom package Description: Using output files of mapReadsToAss2 by STAR the counts were analyzed for differential expression in R using limma voom approach. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_04_mapReadsToAs2-STAR/output/*.counts

Files connected to study: _S_P4_Pcitri_tr2

Short Name: 01_assembly2-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly 2 Description: P citri de-novo transcriptome assembly using SUSPHIRE and mealybug.org RNA-seq datasets pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 02_assembly2-IPS Assay Class: DRY Assay Type: IPS Title: Assembly2 InterProScan Description: InterProScan run for de-novo assembly2 transcripts. AA sequences were obtained by runing transeq and filtering to 3 longest ORFs per transcript. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_01_assembly2-rnaSPAdes/output/soft_filtered_transcripts.fasta

Short Name: 03_mapAs2ToGenome-STAR Assay Class: DRY Assay Type: STAR Title: Mapping assembly2 transcripts to P citri genome Description: Mapping de novo assembled transcripts from SUSPHIRE and Ediburgh RNA-Seq datasets (assembly2) to P citri genome using STARlong. MatchAnnot also run. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: