User: jleehan

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Posts by jleehan

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Interpreting LoFreq output quality score
... The output for LoFreq provides a quality score for each SNP that it calls. However this quality score does not appear to be a typical Phred value score that would max out at 40. I'm seeing values that range from ~50 to 49,314. I am assuming as 49,314 is a high value as expected SNPs are receiving th ...
lofreq next-gen snp sequencing written 4 weeks ago by jleehan0
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Comment: C: Detecting known, low frequency SNPs in bacterial populations
... It should be fairly high coverage, considering I am only sequencing a 505 and 564 bp region and each multiplex is giving me about 1.7M reads, but I will check look into the parameters more ...
written 7 weeks ago by jleehan0
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Comment: C: Detecting known, low frequency SNPs in bacterial populations
... Hi Chris, thanks for your input! I haven't heard of this bam-readcount program before, but it sounds very exciting. I can't seem to find online what the exact output of that program would be. Do you happen to know how that would fit into a VarScan pipeline? My current pipeline (not including qc ste ...
written 7 weeks ago by jleehan0
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Comment: C: Detecting known, low frequency SNPs in bacterial populations
... I used the most basic parameters as I have never used VarScan before: VarScan mpileup2snp $i -o ${SAMPLE}.snp That's the format I'm using ...
written 7 weeks ago by jleehan0
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Detecting known, low frequency SNPs in bacterial populations
... Hi all, I'm using NGS data to observe how a community of congenic bacteria evolve over time. Basically, I'm starting by inputting several different alleles of one gene into the same medium and seeing how that population changes over time by sequencing the DNA of that gene. As far as I can tell, a ...
next-gen snp written 7 weeks ago by jleehan0 • updated 7 weeks ago by Chris Miller20k

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