PRJNA218509 - Good/Bad Cork

SRS481410phellogenNot setThis biomaterial: SRS481410, was created for the analysis: PRJNA218509 - Good/Bad Cork
SRS489988phellogenNot setThis biomaterial: SRS489988, was created for the analysis: PRJNA218509 - Good/Bad Cork
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Teixeira RT, Fortes AM, Pinheiro C, Pereira H. Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue.. Journal of experimental botany. 2014 Sep; 65(17):4887-905.
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
Data Source
Source Name
: PRJNA218509
Source URI