Data

Gene Specific FLAME's Toy data

These datasets are meant for testing the pipeline, testing parameters and for educational purposes.

The toy data directory only contains:

• The filtered BED12 reads from the C666-1 long-read sequencing (Decompress before use).
• The standard EBV (NC_007605.1) GTF reference.

These datasets are the bare necessity for testing the Gene-Specific FLAME module. Toy data for FLAME-GLOW is planned to be amended in a future patch.

Additional compliments for further in-depth analysis using short-read confirmation and canonical splice junction detection needs to be downloaded from public repositories.

These repositories are:

• NCBI's EBV (NC_007605.1) reference assembly sequence in fasta-format which are publically available.

• Edwards, R.H., et al's, short-read sequencing data.

  This data is publically available under the NCBI BioProject ID PRJNA501807.

  The dataset with SRA Accession ID:SRR8133536 was used and is available to download through NCBI's SRA-tools toolkit.

Example on running Gene Specific FLAME with the Toy data

This example will use the EBV non-coding RNA RPMS1 as the target gene.

• Using Gene Specific FLAME with minimal addition will use the following syntax:

./FLAME.py -I C666_LR_01.bed -GTF Epstein-BarrVirus.gtf -G RPMS1

• Using Gene Specific FLAME with canonical splice junction detection will use the following syntax:

./FLAME.py -I C666_LR_01.bed -GTF Epstein-BarrVirus.gtf -G RPMS1 -R [Reference.fasta]

• Using Gene Specific FLAME with shortread confirmation will use the following syntax:

./FLAME.py -I C666_LR_01.bed -GTF Epstein-BarrVirus.gtf -G RPMS1 -B [Shortread.bam]

Example on running FLAME-GLOW with the Toy data

Currently no toy data exists for the FLAME-GLOW pipeline.
This is planned to be amended in a future patch.

FLAME-GLOW's Toy data

Currently, there are no toy data to test the FLAME-GLOW module uploaded.
This is planned to be amended in a future patch.