User: nzs208

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nzs2080
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Posts by nzs208

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Comment: C: Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
... Hi Pierre, Thanks for getting back to me. These supplemental alignments from the same read will not have the secondary flag set, so when I try to filter for primary alignments, I also capture these. But you are saying that there will always be one primary alignment that is not supplemental? How sh ...
written 5 weeks ago by nzs2080
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Comment: C: Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
... They were created with Minimap2. Is this a question that would be more appropriate to ask on the Minimap2 Github? ...
written 5 weeks ago by nzs2080
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Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
... Hi, I've been using Pysam to help me parse bam files. I noticed that in some cases, the Samtools Flag will be set to 0, and the SA tag will also be set. When I use the samtools read.is_supplemental, this will return False. I find this confusing because I would assume that if the SA tag is set, the ...
alignment bam written 5 weeks ago by nzs2080

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