User: pegeot.henri

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Posts by pegeot.henri

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Target mean coverage : Picard Versus Qualimap, why so different?
... Hello, I would like to know if any of you know why the **target mean coverage** is so different when calculated by Picard or Qualimap. For thesame bam and bed files : Exome A ; Qualimap = 127.8 ; Picard = 88.2 Exome B ; Qualimap = 151.9 ; Picard = 104.9 Exome A ; Qualimap = 113.6 ; Picard = 77. ...
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Comment: C: Comparing metrics of two exome: how to interpret higher median coverage but lowe
... > Doesn't Picard HS also output median coverage ? Yes and it is different from qualimap and I have no idea why, for the same data: Qualimap median coverage = 110X ; Picard Median coverage = 80X I know picard does not consider duplicated read, I cannot find out if Qualimap does it... Thank you, ...
written 6 days ago by pegeot.henri0
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Comparing metrics of two exome: how to interpret higher median coverage but lower mean target coverage?
... Hello there, so I am analyzing metrics from two kit of exome sequencing and I have the following: For 100M reads for both exome: **Qualimap: median coverage:** - Exome A = 150X - Exome B = 110X **Picard HS Metrics mean target coverage:** - Exome A = 75X - Exome B = 85X How do you interpret th ...
exome median metrics coverage mean written 6 days ago by pegeot.henri0 • updated 6 days ago by trausch1.2k
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Answer: A: Exome data : drawing a plot showing GC content against normalized mean
... So I have done the following : - Using `bedtool nuc` I have calculated the GC content of each region of my bed file - Using samtools bedcov, I have calculated the average depth of coverage for each region of my bed : `samtools bedcov -Q 30 Intervals.bed sample.bam | sort -k1,1 -k2,2n -k3,3n | awk ...
written 6 days ago by pegeot.henri0
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Comment: A: Exome data : drawing a plot showing GC content against normalized mean
... Is CollectGcBiasMetrics (Picard) what I am looking for ? ...
written 7 days ago by pegeot.henri0
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Exome data : drawing a plot showing GC content against normalized mean
... Hi, I wonder what should I do to obtain a dataset to draw a plot showing GC content against mean depth for exome data (like [this][1]). I have bam files, bed files, fastQ files but I don't even know where I should start. Thanks [1]: https://www.researchgate.net/figure/Normalized-depth-of-covera ...
exome gc content written 7 days ago by pegeot.henri0
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Comment: C: Is it fair to compare 2x75 bp and 2x150 bp exome performances after downsampling
... To give more context I work in an hospital and I am looking for the most performant sequencing kit. This will lead to the choice of a technology for routine use for patients analysis. One of the key metrics I want to investigate is the target coverage efficiency for the same sequencing effort. Conc ...
written 7 months ago by pegeot.henri0
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Comment: C: Is it fair to compare 2x75 bp and 2x150 bp exome performances after downsampling
... I am interested in comparing standard QC metrics. Amongst other things, I am particularly interested in the target Coverage efficiency as a function of number of reads. Downsampling is usually done in such cases as it allows a comparaison with the same amount of sequencing. ...
written 7 months ago by pegeot.henri0
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Is it fair to compare 2x75 bp and 2x150 bp exome performances after downsampling at the same number of reads ?
... Hello, I am performing exome comparisons between different technologies and different sequencing conditions. I have downsampled my dataset for a fair comparison at 5M 10M ..... 60M (M = million of reads). Amongst other things, I compare notably exomes with 2 x 150 bp vs 2 x 75 bp. But in both case ...
exome ngs sequencing written 7 months ago by pegeot.henri0
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Comment: C: How to filter VCF with HRun > 8 and AB > 0.2 and AB < 0.2
... Hello again, I have made some progress to filter vcf based on allelic balance. I used the tools vcffilterjdk with the following command line : java -jar vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD()).map(G->G.getAD()).allMatch(A->A.length>1 &&am ...
written 7 months ago by pegeot.henri0

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