User: chris.bird

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chris.bird0
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Posts by chris.bird

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Answer: A: Does BWA mem ever edit data
... it can clip bases, you'll want to relax the defaults reads could also be filtered if they don't map to the reference genome given that a bam file has more info than a fastq file, this probably won't work search on binary fastq for a better solution ...
written 5 months ago by chris.bird0
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bwa mem -T (alignment score) not doing anything
... I'm trying to control which reads are mapped to a reference genome by adjusting the the -T parameter in bwa mem, which is the minimum acceptable alignment score. The only problem is that reads with an alignment score below the threshold are being mapped anyway. I can see this when using samtools ...
genome sequence snp written 5 months ago by chris.bird0
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Inferring Ploidy or Copy Number from Allele Balance?
... I'm helping a colleague analyze their RAD / GBS data from a flowering plant. They thought their genome was 2n based on flow cytometry in the samples I'm analyzing and a karyotype or 2 from the literature. After genotyping, however, there's excess heterozygosity and a lot of loci are not in HWE. W ...
genome snp sequencing written 5 months ago by chris.bird0

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