Assembled mRNAs from potato genotypes contrasted for their hexanal isomerase activity

<p>From PacBio and Illumina mRNA-seq coming from leaf total RNA isolated from three <em>Solanum tuberosum</em> genotypes (Desiree, Phureja153 and S869), mRNA isoforms were assembled.</p> <ul> <li><strong>Phureja153:</strong> low (3Z):(2E) hexenal isomerase activity</li> <li><strong>Desiree:</strong> mid (3Z):(2E) hexenal isomerase activity</li> <li><strong>S869</strong>: high (3Z):(2E) hexenal isomerase activity</li> </ul> <p>&nbsp;</p> <p><strong>== Step1: PacBio subreads to FASTA and GTF annotation == </strong></p> <p>For each genotype, a FASTA file and a GTF annotation file are available. File is called &quot;<a href="https://zenodo.org/api/files/e5e70d61-d4cc-4896-8eb1-b41447b8859d/pacbio_assembled_isoforms.tar.gz?versionId=a91bb81f-3442-427c-be96-190f19b4bf3c">pacbio_assembled_isoforms.tar.gz</a>&quot;.</p> <p>Pipeline used: <a href="https://github.com/SilkeAllmannLab/pacbio_snakemake/releases/tag/v0.1.0">https://github.com/SilkeAllmannLab/pacbio_snakemake/releases/tag/v0.1.0</a></p> <p>Raw PacBio data submitted to NCBI EBI ENA under accession PRJXXX.</p> <p>=== Step 2: SQANTI QC ====</p> <p><a href="https://github.com/ConesaLab/SQANTI3/wiki/Introduction-to-SQANTI3">SQANTI3</a> was run on these three PacBio assembled sets of transcript to correct them.</p> <p>The corrected transcripts and related SQANTI3 info are available in the &quot;<a href="https://zenodo.org/api/files/e5e70d61-d4cc-4896-8eb1-b41447b8859d/sqanti_corrected_transcripts.tar.gz">sqanti_corrected_transcripts.tar.gz</a>&quot; file.</p> <p>&nbsp;</p> <p>&nbsp;</p>