Strange alignment (and seemingly incorrect score) for ONT cDNA alignment #1257
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If the sequences between two anchors can't be aligned well, the score can be negative. This is expected. |
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Thanks Heng, One more related query if it's not too much trouble. I can't seem to get to -19 using the CIGAR string, using the default match, mismatch, and gap penalties listed in the manpage. Is the gap cost gap open + (gap len * gap extend) (which seems to underestimate the score) or gap open + ((gap len - 1) * gap extend) (which seems to overestimate the score)? Thanks, |
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It is open+len*ext. Nonetheless, the longest gap length is 86. This will trigger the dual gap penalty. |
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Thank you, @lh3! I can confirm that I, in fact, get the appropriate score (-19) when properly accounting for the dual gap penalty. While I realize that you're not in anyway affiliated with Specifically, Do you have any idea why Edit: Additionally, I observe the same behavior (only 2 mappings) if I map the read using |
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The other two alignments are secondary. |
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Hi Heng, But is there a reason they would not be reported? Is there a way I can get them (via mappy, or minimap2-lite, or via minimap2 as a library more generally)? I am not interested in supplementary alignments in this case (though I am getting one), but do want secondary alignments. In mappy and minimap2-rs I am requesting up to 100 alignments for each query. |
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What is your mappy script? |
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Note you added |
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Hi Heng, My mappy script is very minimal: Where, above the |
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Hi @lh3, Thanks for your help on this. I debugged it a bit more and I discovered that the differences here are due to the fact that both This accounts for the issue I was observing. In order to allow matching the output of command-line Thanks! |
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Closing as #1260 has been merged. |
Hi Heng,
I was trying to track down a number of small differences I encounter between standard alignment using
minimap2and using theminimap2-rscrate in ouroarfishtool. My working assumption is that command-lineminimap2is the "ground truth", and so any differences are strange (sinceminimap2-rsjust calls tominimap2as a library).Anyway, I found a minimal reproducible example, and when I investigated, much to my surprise, I can't even really understand the
minimap2output itself. I'm aligning against a transcriptome reference (which can be obtained here). A file containing the read is here.I map with the following command:
then, if I look at the resulting
bamfile, I get:While there may be several strange things, it's the first alignment that most confuses me (the one marked as primary)
The alignment score is
-19. Inminimap2-rsthis shows up asu32::MAX - 18because the score is treated as an unsigned integer when it is returned (which obviously is not right). However, I don't see how the reported score of-19makes sense here. If I process the CIGAR string itself, I get a much higher score.Any thoughts about why the reported alignment score is what it is, or how to fix this? Seemingly, an alignment with a score of
-19shouldn't even be reported in this context.Thanks!
Rob
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