Summary
Name
Persea americana - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Persea americana
Data Source
Date Performed
Tuesday, August 6, 2019 - 15:06
Program, Pipeline, Workflow or Method Name
De novo assembly
Program Version
2.4 (P.americana)
Publication
Kilaru, A., Cao, X., Dabbs, P.B., Sung, H.J., Rahman, M.M., Thrower, N.A., Zynda, G., Podicheti, R., Ibarra-Laclette, E., Herrera-Estrella, L.R., Mockaitis, K., & Ohlrogge, J.B. (2015). Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp. BMC Plant Biology.
Description and Download
Description: 
Persea americana's transcriptome was assembled from 7 biosamples located on NCBI using bioproject PRJNA253536. FastQC was used to determine overall read quality, detect Illumina primer sequences, and identify any regions that look incorrect. Trimmomatic was then used to remove any Illumina primer sequences, after which RCorrector was used to remove any minor errors that Illumina may have caused. After all the files are cleaned, Trinity was used to assemble the transcriptome, Skewer and STAR were used for refinement and alignment of the transcriptome.

Downloads:

Cds (fasta format)
Peptides (fasta format)
gff3 file
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