SRP002613 - Good/Bad Cork

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRS083080phellogenNot setThis biomaterial: SRS083080, was created for the analysis: SRP002613 - Good/Bad Cork
SRS083081phellogenNot setThis biomaterial: SRS083081, was created for the analysis: SRP002613 - Good/Bad Cork
Publication
Paiva, J.A., Fevereiro, P., Marques, P. et al. Deciphering cork formation in Quercus suber. BMC Proc 5, P172 (2011).
Summary
Name
SRP002613 - Good/Bad Cork
Description

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
SRP002613 - 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
: SRP002613
Source URI
: https://www.ncbi.nlm.nih.gov/sra?term=SRP002613