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

Question

[biolab]

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!

[GenoMax]

See this for more: Does Bowtie2 Preform Unique Mapping
If you are interested in removing multi-mapped reads then see @Devon's answer here: How to extract unique mapped results from Bowtie2 bam results?

[biolab]

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

Answer 1

[WouterDeCoster]

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.

[biolab]

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

[ATCG]

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?