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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
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How are mitochondrial reads aligned? #416

Open imk1 opened 1 year ago

imk1 commented 1 year ago

I noticed that the pipeline now has new mitochondrial read alignments. Do these alignments happen before the alignment to the nuclear genome, do they happen in parallel to the alignment for the nuclear genome, or are the alignments to the nuclear genome and mitochondrial genome separated after the alignment to the nuclear genome has been completed? Thanks!

akundaje commented 1 year ago

Alignment is done jointly (nuclear + mito). Then mito reads are separated out.

-Anshul.

On Tue, May 9, 2023 at 8:15 AM Irene Kaplow @.***> wrote:

I noticed that the pipeline now has new mitochondrial read alignments. Do these alignments happen before the alignment to the nuclear genome, do they happen in parallel to the alignment for the nuclear genome, or are the alignments to the nuclear genome and mitochondrial genome separated after the alignment to the nuclear genome has been completed? Thanks!

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