README.md

fiberseq-qc

QC plots and statistics

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Software Setup

# download the software:
git clone https://github.com/fiberseq/fiberseq-qc.git
cd fiberseq-qc

# install external dependencies using:
conda create -n fiberseq-qc
mamba env update -n fiberseq-qc --file env/qc.yaml

Then, activate your environment
conda activate fiberseq-qc

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Example Run

src/runall-qc.tcsh my-output-dir PS00246 fiberseq.ft.bam

where fiberseq.ft.bam was produced using the ft predict-m6a command

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Output

The main output is a page that ends in overview.html that you can open in your browser.
On the left side is a series of pertinent histogram and other analysis images with statistics.
On the right side is a blow-up of any image that you mouse over on the left.