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ekimb / mapquik

Efficient low-divergence mapping of long reads in minimizer space
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Mapping results are wrong #20

Open WataruTsutae opened 2 months ago

WataruTsutae commented 2 months ago

Mapping results are wrong. What is happening ?

ex)

m64379e_240705_043448/74/ccs GAAGATATAACCAGTGGCCTTCAAATACATTCCTCTTTCGAGATTATCTGTCTTTAGCAT TCTCAGTTATGAGCTTAATGCCTTCTTGGTCATTTACAAGGTATCAGACAGCAAATACCA GGAAATATGACATTGCTTTCAACTTGTGCATTATATGGTATTAGTACTGGTGATGATGCC AACAGTTAAAAATACACTTCAGGTGCACCCACTGTCCCCTTCTCTCTTTCACCCCCAACT GCTACCACAAGATAGAATAACTAGCACACTAGAACAAGCAATGCAGACTTAAAAAATGAT AGCTATAACCTGAACCAGTGGTCAATATTAGCCTCGCTTAGAAATTGATCAAGGACTTGC ATCAATTCACAAAGCATTTATTAAAAAAAATCATCTGAATCTCAGTAAGACCAGGGAGAT TTCTGGCATTTTAACTCATCCTATTCCCATCCTCTCTCCTCACTTCTGTGGTAAACTTGA AAACCAACAACTCACAATCACACTGAAAACCAGCAGTCTTGCAGTCACTGGAGGGGTCAG AATGGGACTGGAACACTTCCAAAGCCTCATCCCCAGAGAATTGTCATTATTTGACTGGTC TGGCAGTTTCCTGGAAACCCCCACTCACAGAATTTCTCTTTAATTCACCTGACTCAGAGC m64379e_240705_043448/96/ccs AATATATAAATAATTATACAACTCACCATAACGTAGAATCAGTGGGAGCCCTGAGCTTGT TTTCCTGCAACTAGATGGTCCCAACTAGACCAGGTGATGGGAGACAATGACAGATCATTA GGCATTAGATTATCATAAGGAGCATACAACCTAGATCCCTTGCATGTGCAGTTAATAATA GGTTTTGCACTTCTATGAGGATCTAATGCGGCCTCTGATCTGACAAGGGGCGGAGCTCAG GCAGTAATGGGAGCAATGGGGAGCGGTTTTCAATACAGATGAGGCTTTGGTCACTTGCCT GCCTTTCACCTCCTGCTGTGCAGCTTGGTTCCCAACAGGCCACGGACTGGTGGTCCTTGG CCTGGGAGTTGGGGACCCCTGCTCTAAATAATTGTATTAATTAGAATATAGGTTTGGCTG CCCTAACAAGGACTCAGACTAACTTGGCTGACATTGACAGACAATTCTTTCTCTTTATAA AACAGTCTAGGCAACTCCATGATGTTGAGGACCCAGATCCTTCTTTATTGTTTTTCCTCC ATTCTTCAGATGTGGCCTTCATCCACATGGGCAATGATGGCTTTCCAGCATATCTGCACA GGGCAATGGAGAAAGGGAGGCATGCTTTGGAAGCTGTGCACAGCACTTCCGTTCACACCC CAGTGGCGAGAACTTAGCTGTGTGGCCACATCTAGCTGGAATGGAGGCTGGCTGGGTAGA CATGTATCCAGTTTATAACTGGGGGCTTCCTGGAAGGGAGAACAGACTTTGGGGTAGCCC

PAF file m64379e_240705_043448/74/ccs 11573 0 11572 - chr9 141162611 98972906 98984537 1 141162611 0 m64379e_240705_043448/96/ccs 6912 0 6911 + chr18 81980750 30052116 30058942 1 81980750 0

Blast Result m64379e_240705_043448/74/ccs Human DNA sequence from clone RP4-540A13 on chromosome Xq22.1-22.3, complete sequence Sequence ID: FO393406.1Length: 85371Number of Matches: 1 Range 1: 26660 to 27319

m64379e_240705_043448/96/ccs Homo sapiens chromosome 3 clone RP11-745O8, complete sequence Sequence ID: AC107625.3Length: 42001Number of Matches: 1 Range 1: 23875 to 24654

rchikhi commented 2 months ago

Did you convert your input and reference FASTA to 1-line format as per https://github.com/ekimb/mapquik/issues/17#issuecomment-1895882175 ?