User: bas1993

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bas199310
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Posts by bas1993

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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... To give some more background information, I didn't knock in the gene myself but a whole plasmid is integrated in the chromosome by an external company in a food bacteria. The documentation of this modification is not correct and that is why we sequenced it. The plasmid is around 7000 basepairs and I ...
written 9 weeks ago by bas199310
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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... I already did an assembly and in the .gfa files it looked like circular contig that is connected to the chromosome. So I hypothised that maybe the assembly was influenced by some of the reads that are shorter than the modification. That is why I extracted all the reads that are longer than the modif ...
written 9 weeks ago by bas199310
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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... But will I not get the same problem as with other mappers. I know the genetic modification is present in the reads, but I would like to know if it is present multiple times (or 1 time completely and then half of the sequence). ...
written 9 weeks ago by bas199310
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How to see how many times a sequence of ~7000 bp occurs in long reads?
... So I have pacbio and MinION reads and I want to know if a genetically modified region is 1 time present or multiple times. Normal mapping doesn't give me the answers that I want as the reads are soft-clipped on the known sequence so I have no information about what else is in the read. So instead of ...
alignment next-gen sequencing written 9 weeks ago by bas199310 • updated 14 days ago by Biostar ♦♦ 20

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