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This describes an alignments of a read against itself running from end to end, but clearly not the optimal alignment between the two regions specified.
There are two versions.
minimap2 was run with as
minimap2/minimap2 -ax ava-pb dup.fasta dup.fasta
where dup.fasta contains a single read (synthetic E. coli, though I think this should not matter).
It is not recommended to generate CIGAR for read overlapping because 1) generating CIGAR for every overlap is very slow; 2) it is usually not necessary to have cigar for read overlapping. SAM is also the wrong format for read overlapping. No read overlappers output SAM.
On your example, minimap/minimap2 ignore anchors with the same position if the read name is the same, so you shouldn't see perfect alignment. However, with CIGAR on, alignment extension may still produce a nearly perfect alignment from different seeds. This is a problem with minimap2, which I will try to fix at some point. Thanks.
Hi,
I see the following somewhat weird data (SAM format) coming out of minimap2:
This is weird for two reasons:
minimap2 was run with as
where dup.fasta contains a single read (synthetic E. coli, though I think this should not matter).
The single read in dup.fasta is
Best,
German
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