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HISAT2: does the parameter -k 1 means unique mapping?

Hi, everyone,

The -k <int> parameter in HISAT2 is explained by the following in the manual: It searches for at most <int> distinct, primary alignments for each read.

If I use -k 1, does it mean unique mapping? Thank you very much!

hisat2
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updated by WouterDeCoster WouterDeCoster • written by biolab biolab

Thank you very much, genomax, these posts are very helpful.

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written by biolab biolab

1 answer

As far as I understood it will then only produce 1 alignment per read - even if there are multiple locations in the genome to which that read would fit. So you would indeed get unique mappings, but that's cheating and incorrect.

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written by WouterDeCoster WouterDeCoster

Hi, WouterDeCoster, thank you very much for your explanations.

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written by biolab biolab

Is it incorrect to include all reads even those that map >1 times? I have always kept uniquely mapped. Also is there an option to keep only uniquely mapped using HISAT2?

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written by ATCG ATCG

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