User: Darren Lin

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Darren Lin0
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Posts by Darren Lin

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About structure variants simulation
... Guys, I am trying to use DWGSIM to generate some simulation paired-end reads with a VCF file of candidate mutations. I use the command like : dwgsim -1 101 -2 101 -v true.vcf ucsc.hg19.fasta read But it gives an error message "out of order [chr1, 788889]". The error message indicates this line in t ...
sv simulation written 10 weeks ago by Darren Lin0 • updated 10 weeks ago by Kevin Blighe13k
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Comment: A: Extreme large insert size of BWA alignment
... hm....thanks, but I can not just filter "properly paired" flag. I can probably set a threshold to limit the maximum deletion. ...
written 11 weeks ago by Darren Lin0
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Extreme large insert size of BWA alignment
... The BAM file I am dealing with consist some alignments with extremely large insert size. For example: H06HDADXX130110:1:1214:13197:7463 145 20 1361711 60 41S147M62S = 61590101 60228245 H06HDADXX130110:1:1214:13197:7463 97 20 61590101 60 242M8S = 1361711 -60228245 What's going on with thi ...
bwa alignment forum written 11 weeks ago by Darren Lin0
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Forum: Questions about the mechanism behind breakdancer-max
... Hi all, I use breakdancer-max to run chr20 of sample NA12878. After I read the paper, I was confused about one sentence, which said "The algorithm searches for genomic regions that anchor substantially more anomalous read pairs(ARPs) than expected on average." And before search, each read pair is a ...
structure variant forum breakdancer written 16 months ago by Darren Lin0

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