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!
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?
Thank you very much, genomax, these posts are very helpful.
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.
Hi, WouterDeCoster, thank you very much for your explanations.
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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