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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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Recover missing alignment #979

Open tbenavi1 opened 2 years ago

tbenavi1 commented 2 years ago

Hello,

I am wondering how I can recover an alignment that exists when mapping to a reference with a single sequence, but which does not exist when mapping to a reference with multiple sequences which includes the first sequence.

Specifically, when I map (using map-hifi preset) the read SRR10238607.1042201.fq to the sequence lcl|NC_004354.4_mrna_NM_001298349.1_4046, I get the following alignment:

SRR10238607.1042201     16      lcl|NC_004354.4_mrna_NM_001298349.1_4046        279     60      13542S123M13I3M1D170M1I2M1I2M2D24M4I1M5I357M1I6M1D27M7084S

However, when I map to GCF_000001215.4_Release_6_plus_ISO1_MT_rna_from_genomic.fna.gz which includes the above sequence, I do not get that alignment. I have tried changing the parameters but to no avail. Adding "-P" does recover more alignments, but I am still missing the one above.

Here are the files: SRR10238607.1042201.fq.gz 4046_transcript.fa.gz GCF_000001215.4_Release_6_plus_ISO1_MT_rna_from_genomic.fna.gz

Thanks for any assistance.

tbenavi1 commented 2 years ago

Any ideas? I'm sure it has something to do with repetitive alignments. Adding "-M0" doesn't recover the alignment, unfortunately.