User: jleehan

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Posts by jleehan

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Comment: C: Artemis Comparison Tool "error while reading: cannot understand comparison file
... Okay, thanks! I already have the BAMs ...
written 19 days ago by jleehan0
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Comment: C: Artemis Comparison Tool "error while reading: cannot understand comparison file
... I am BLASTing my reads against the reference genome ...
written 20 days ago by jleehan0
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Comment: C: Artemis Comparison Tool "error while reading: cannot understand comparison file
... Here are the first 12 lines: FS10000238:8:BPA73012-1025:1:1101:12160:1970/1 NC_000964.3 100.000 145 0 0 7 151 1 145 6.31e-73 268 FS10000238:8:BPA73012-1025:1:1102:0:0/1 NC_000964.3 100.000 145 0 0 6 150 1 145 6.26e-73 268 FS10000238:8:BPA73012-1025:1:1106:0:0/1 NC_000964.3 100.000 144 0 ...
written 20 days ago by jleehan0 • updated 20 days ago by Joe14k
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Artemis Comparison Tool "error while reading: cannot understand comparison file format"
... CI am trying to visualize the differences in the genome of an evolved strain of *Bacillus subtilis* and have attempted using numerous methods including mauve, BRIG and ACT. I haven't been able to get any of them to work, but feel as though ACT has been as close as I've been able to get. To generate ...
act artemis comparative genomics written 21 days ago by jleehan0
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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 8 months 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 9 months 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 9 months 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 9 months 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 9 months ago by jleehan0 • updated 9 months ago by Chris Miller21k

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