PRJNA218509 - Good/Bad Cork

Resource Type
PRJNA218509 - Good/Bad Cork

"The present work establishes a comparison of phellogenic genes differentially expressed during the development of cork of good and bad quality making use of Roche 454-pyrosequencing."

FASTQ files were obtained from the NCBI database using the SRAtoolkit-2.9.4. Tags were removed using TagCleaner-0.16 and high quality reads were filtered using Trimmomatic-0.38. Mapping to the reference genome of Q.suber (NCBI Sequence Read Archive SRP111728 (2017)) was performed using Gmap-2018-07-04 and gene expression in TPM (transcripts per million) was calculated using the counts obtained from featureCounts included in SubRead-v1.6.3.

Program, Pipeline, Workflow or Method Name
PRJNA218509 - Good/Bad Cork
Program Version
Gmap-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Date Performed
Thursday, April 11, 2019 - 12:01
Data Source
SRS481410Phellogen (good quality cork)Not setThis biomaterial: SRS481410, was created for the analysis: PRJNA218509 - Good/Bad Cork
SRS489988Phellogen (bad quality cork)Not setThis biomaterial: SRS489988, was created for the analysis: PRJNA218509 - Good/Bad Cork