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VDI RNA Seq Handler

This is the VDI Handler for RNA Seq datasets. These datasets contain FPKM data in .txt files, and optionally bigwig files used for genome browser tracks.

See the VDI Handler Example repo for background.

For more details about the scripts themselves and their inputs and outputs see the VDI Plugin Handler Server readme.

The import script does its best to validate the dataset. On the assumption that the dataset is provided by the VEuPathDB RNA Seq Exporter, we hope that it was constructed validly. It is possible the validator will miss ways the dataset could go wrong.

Here is a manifest file from a stranded dataset

SRR5260550.fastq-forward	SRR5260550.fastq-forward.bw	firststrand
SRR5260550.fastq-reverse	SRR5260550.fastq-reverse.bw	secondstrand
SRR5260551.fastq-forward	SRR5260551.fastq-forward.bw	firststrand
SRR5260551.fastq-reverse	SRR5260551.fastq-reverse.bw	secondstrand
SRR5260552.fastq-forward	SRR5260552.fastq-forward.bw	firststrand
SRR5260552.fastq-reverse	SRR5260552.fastq-reverse.bw	secondstrand
SRR5260550.fastq-one	SRR5260550.fastq-one.txt	sense
SRR5260550.fastq-two	SRR5260550.fastq-two.txt	antisense
SRR5260551.fastq-one	SRR5260551.fastq-one.txt	sense
SRR5260551.fastq-two	SRR5260551.fastq-two.txt	antisense
SRR5260552.fastq-one	SRR5260552.fastq-one.txt	sense
SRR5260552.fastq-two	SRR5260552.fastq-two.txt	antisense