User: Adam R

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Adam R20
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New User
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United States
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4 years, 9 months ago
Joined:
5 years, 9 months ago
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Posts by Adam R

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Comment: C: Tool to separate two genotypes from mapped Illumina reads?
... Thanks for the ideas. Based on read depth, it does not look like a duplication, but I'll probably incorporate that possibility into any systematic analysis that I do. And yes, a less aggressive assembler could allow me to recover both genotypes for the diverse regions. ...
written 4.8 years ago by Adam R20
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Comment: C: Tool to separate two genotypes from mapped Illumina reads?
... Thanks. BBSplit would work for one of my studies (where one strain may be invading a region with another strain). The polymorphisms are clustered together, and I was only hoping to link them together within each region (on the order of 1kb in size) ...
written 4.8 years ago by Adam R20
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Tool to separate two genotypes from mapped Illumina reads?
... Dear BioStars, I have a few Illumina datasets where I've seen a puzzling pattern in my mapped reads, and would appreciate some tips as to how to figure out what's going on. These datasets represent bacterial cultures. I have mapped the reads to genomes that are expected to be very closely related - ...
genome bacteria mapping written 4.8 years ago by Adam R20 • updated 4.6 years ago by russianconcussion30
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Comment: C: Biopython: Is It Possible To Update Only Sequence In A Seqrecord Object?
... If you are hitting an error relating to letter annotations (e.g. "You must empty the letter annotations first!"), you can copy them to a temporary dict object while you modify the seq, clear them, and then copy them back to the SeqRecord afterwards. ...
written 5.4 years ago by Adam R20
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Answer: A: Equivalent Blast And Blast+ Commands
... There's a nice diagram in the manual http://www.ncbi.nlm.nih.gov/books/NBK1763/#_CmdLineAppsManual_Appendix_A_Conversion_ ...
written 5.4 years ago by Adam R20

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