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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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output unmapped reads #65

Closed mictadlo closed 7 years ago

mictadlo commented 7 years ago

Hi Does GraphMap output unmapped reads, because I try to remove contamination from PacBio reads?

Thank you in advance.

Micha

isovic commented 7 years ago

Hi Micha,

Yes - for every read in the input dataset, GraphMap will generate at least one output alignment line. If a read was not successfully mapped, it will be reported as unmapped via the SAM flag (value equal to 4).

Best regards, Ivan.

mictadlo commented 7 years ago

Thank you