How are mitochondrial reads aligned?

[imk1]

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]

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

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-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! — Reply to this email directly, view it on GitHub <#416>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDWEMNGCJZZNT6IK3I3UTXFJNPXANCNFSM6AAAAAAX3OKNSY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>