Assembled mRNAs from potato genotypes contrasted for their hexanal isomerase activity
Description
From PacBio and Illumina mRNA-seq coming from leaf total RNA isolated from three Solanum tuberosum genotypes (Desiree, Phureja153 and S869), mRNA isoforms were assembled.
- Phureja153: low (3Z):(2E) hexenal isomerase activity
- Desiree: mid (3Z):(2E) hexenal isomerase activity
- S869: high (3Z):(2E) hexenal isomerase activity
== Step1: PacBio subreads to FASTA and GTF annotation ==
For each genotype, a FASTA file and a GTF annotation file are available. File is called "pacbio_assembled_isoforms.tar.gz".
Pipeline used: https://github.com/SilkeAllmannLab/pacbio_snakemake/releases/tag/v0.1.0
Raw PacBio data submitted to NCBI EBI ENA under accession PRJXXX.
=== Step 2: SQANTI QC ====
SQANTI3 was run on these three PacBio assembled sets of transcript to correct them.
The corrected transcripts and related SQANTI3 info are available in the "sqanti_corrected_transcripts.tar.gz" file.
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