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Will circular DNA be reported? #353

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ZeweiSong opened this issue Mar 29, 2023 · 3 comments
Open

Will circular DNA be reported? #353

ZeweiSong opened this issue Mar 29, 2023 · 3 comments

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@ZeweiSong
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ZeweiSong commented Mar 29, 2023

Hi, we have found in our assembled results some contigs have identical first and last 141 bp, which is the longest kmer length we use. Can this kind of contigs be a real circular strucuture or simply an artifact?

For example, this is one of those contigs, the first and last 141 bps in bold:

ctg@k141_1642
AGCCGGCCCTGGGTCCGGTTGATCAGCACGGTGGTGTTCTGAAGCGACAGGAGGCTGTCGCGCACGGCAGCCGAAAGGGTGATCTCAGCCATTGCTGTACCTCGTTTCTAGGGTGCCCTCAACCGGGGCAATCGCTGCACGTGGAGGGATTCTCCCTCCGCGGCGGACGGTCATGAAGGCAGAGGTAAGCGGTGGGCAGCCGGTGCGTAAATTATCCACACGCATAAGGCCGCCGCGGCGCCCCCGCCGGCCAAGGAAAGGAGGGCGCCGGGCCCCCCTTTCCCGCCTAGGGCGATACCAGCCTAGCGGAAGAGCGCCAGGATCCCCTGCTCCGCCTGGCCGGCGAACGACAGGGCCTGGACGCCGAGCTGCTGGCGGGTCTGCAGGGCCAGCAGGTTGGCGCCTTCCTCGTTGAGGTCGGCCAGGGTCAGCTTGTCGGCGCCCGTCTGCAGGGTGTTCACGTAGCTCTCGGTGAACTCGAGACGGGTCTGCAGCAGCGCCACGTTGGAACCGAGGGTCTTGGTCTTGGTGCGCAAGGTGTCCAGGGCCGATTGAAGGTCGGTCACCAGGCCGTTGATTTCGGTGGTGAGCGTGGCGTCGATGTAGTACTGCCCGACAACGTCGCCAACGGTGATGCTGATGCCGGTGGTGATGCCCCCGAATTCCGCCTCACCGTCGCTGATTTTGCTGGCGACCTCGATGGTGAAGCTGAACGTTGTGCCCACGGCAATGACCTGGGTGAGGGCGAACGTAGTCGCCGTGGCCCCGCCGCCCACCGTGCCCACGCTGACGGTCACGGTATGGGTGCCGTAGAGGAACGTGAAATCGCCCGCGGCGCTGAAGGTGAAGGCGGTCGCGCCGGCATAGGTGATAGTGAGCGTCGAGCCGGTGGAGATGCTCACGCCGGTGGCGAAGTCATAGGACACGTTGAATGCTACATCACCGGTCAGCGCCACCGCCGTCAACGCGGTGCGGATGGCAAGGCCGGCGCCGCCTTCGGTCACGTCCACCGAATTGACGACCAGGGTGGACGAGGTGTCGGTGCTGAACTCGACCGTCAGCTTCTCGCCGGTGCCGTTGATCAGGTTCAGGCCCTGAAAGTCGGTGTCCTTGGCCAGGTTGGCGATCTGGAGGCGCAGGTCGTTGAACTGGCTGACCAGCTCGGCGATGGTGCTCGACGTCGCCGACTTGGCCGACACCGCGAGGCCCTTCATCTGGCGGACGATGGCGTCGATCGCCTCGGTGCCGTCCAGGGCCGCCGTCAGGCTGCTGATGCCCTGGTCGATGCCCGCCTTCTTGTCATCGAAGTCCGACGCCCGGTCGGCAAGGGTCTTCGCCTCGAAGAACTTGATCGGGTCGTCGATGGCGCTGGCCACCGACAGCCCGGTGGCCAGCCGGCCCTGGGTCCGGTTGATCAGCACGGTGGTGTTCTGAAGCGACAGGAGGCTGTCGCGCACGGCAGCCGAAAGGGTGATCTCAGCCATTGCTGTACCTCGTTTCTAGGGTGCCCTCAACCGGGGCAATCGCTGCACG

Thanks!

@ZeweiSong ZeweiSong changed the title will cirrcular dna be reported Will circular dna be reported? Mar 29, 2023
@ZeweiSong ZeweiSong changed the title Will circular dna be reported? Will circular DNA be reported? Mar 29, 2023
@alienzj
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alienzj commented Apr 3, 2023

image

@alienzj
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alienzj commented Apr 3, 2023

image

@alienzj
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alienzj commented Apr 3, 2023

It looks like this 141 bp sequence can not be identified from SRA microbe and fungi datasets.

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