47 lines
2.0 KiB
Markdown
47 lines
2.0 KiB
Markdown
#### 1. Alignment different with option `-a` or `-c`?
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Without `-a`, `-c` or `--cs`, minimap2 only finds *approximate* mapping
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locations without detailed base alignment. In particular, the start and end
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positions of the alignment are impricise. With one of those options, minimap2
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will perform base alignment, which is generally more accurate but is much
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slower.
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#### 2. How to map Illumina short reads to noisy long reads?
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No good solutions. The better approach is to assemble short reads into contigs
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and then map noisy reads to contigs.
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#### 3. The output SAM doesn't have a header.
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By default, minimap2 indexes 4 billion reference bases (4Gb) in a batch and map
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all reads against each reference batch. Given a reference longer than 4Gb,
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minimap2 is unable to see all the sequences and thus can't produce a correct
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SAM header. In this case, minimap2 doesn't output any SAM header. There are two
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solutions to this issue. First, you may increase option `-I` to, for example,
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`-I8g` to index more reference bases in a batch. This is preferred if your
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machine has enough memory. Second, if your machines doesn't have enough memory
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to hold the reference index, you can use the `--split-prefix` option in a
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command line like:
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```sh
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minimap2 -ax map-ont --split-prefix=tmp ref.fa reads.fq
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```
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This second approach uses less memory, but it is slower and requires temporary
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disk space.
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#### 4. The output SAM is malformatted.
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This typically happens when you use nohup to wrap a minimap2 command line.
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Nohup is discouraged as it breaks piping. If you have to use nohup, please
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specify an output file with option `-o`.
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#### 5. How to output one alignment per read?
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You can use `--secondary=no` to suppress secondary alignments (aka multiple
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mappings), but you can't suppress supplementary alignment (aka split or
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chimeric alignment) this way. You can use samtools to filter out these
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alignments:
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```sh
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minimap2 -ax map-out ref.fa reads.fq | samtools view -F0x900
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```
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However, this is discouraged as supplementary alignment is informative.
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