Published April 28, 2019 | Version v3
Dataset Open

Alignment and mapping methodology impact transcript abundance estimation

Authors/Creators

  • 1. Stony Brook University
  • 2. University of Maryland
  • 3. Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics
  • 4. University of North Carolina
  • 5. Carnegie Mellon University

Description

SRR109.txt -> list of accession numbers used for experimental analysis.

simulatedquants -> Bowtie2 pipeline quantification results on the 109 samples, that are used to simulate datasets for futher analysis.

scriptsSimulate -> scripts to generate simulated data using the 109 quantification results on real data. The "runme.sh" file can be executed to generate a "data" folder with all the simulated reads and ground truth count and TPM values.

table1Data -> fasta and true abundance files for 10 replicates of simulated data (from human transcriptome GENCODE v29) used to generate table 1 of the manuscript.

table2Data -> fasta and true abundance files for 10 replicates of simulated data (from mouse transcriptome PWK variant) used to generate table 2 of the manuscript.

refFastas -> the human and mouse reference fasta files containing the sequence-similar decoy sequences, which can be used to construct the salmon index for SA.

Files

SRR109.txt

Files (28.5 GB)

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