Question: HISAT2: does the parameter -k 1 means unique mapping?
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gravatar for biolab
2.3 years ago by
biolab1.1k
biolab1.1k wrote:

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 • 1.4k views
ADD COMMENTlink modified 2.3 years ago by WouterDeCoster41k • written 2.3 years ago by biolab1.1k
1

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?

ADD REPLYlink written 2.3 years ago by genomax72k

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

ADD REPLYlink written 2.3 years ago by biolab1.1k
1
gravatar for WouterDeCoster
2.3 years ago by
Belgium
WouterDeCoster41k wrote:

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.

ADD COMMENTlink written 2.3 years ago by WouterDeCoster41k

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

ADD REPLYlink written 2.3 years ago by biolab1.1k
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