User: lait

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lait80
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Posts by lait

<prev • 53 results • page 1 of 6 • next >
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processing parent-child duos
... Hi, Can anyone provide me with additional helpful hints to carry the following analysis: I want to analyse the variants of children with a cancer, where only one of the parents is available. So I do have the fastq/bam/vcf files of duos (child + one parent). I assume one can only know the inherite ...
exome sequencing ngs duos denovo written 13 days ago by lait80
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haplotype phasing in duos
... Hi I have worked with readbackedphasing to phase haplotypes in trios. Now, I have those cases where one of the parents is missing, are you aware of any tool that can handle haplotype phasing in duos? or is there any kind of solution - work-around - for this problem? Many thanks. ...
haplotype phasing duos rna-seq trios written 29 days ago by lait80
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Comment: C: low coverage & BAF plots have three peaks
... all others with three peaks are similar to this one. ...
written 9 weeks ago by lait80
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Comment: C: low coverage & BAF plots have three peaks
... here is a [link][1] to the figure. [1]: https://app.box.com/s/ld39yb3eebrk6scjcu8myalk8yth0xsm ...
written 9 weeks ago by lait80
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Comment: C: sample mixing when demultiplexing
... thanks a lot. Using your script, I am sure now that there were no mix between the sequences. In this regard, do you have an explanation for the following: I processed the vcf files, and calculated the b-allele frequency for the heteroz. mutations. when plotting the frequency graph, most of the plo ...
written 10 weeks ago by lait80
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Comment: C: sample mixing when demultiplexing
... ok thanks.. I added an important point in the Edit section.. could the error have happened then in the next step after demultiplexing? which is collecting samples across different lanes? if so, then I would come back to my previous question, if it is applicable here to check if there were sample mix ...
written 10 weeks ago by lait80
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sample mixing when demultiplexing
... How is it possible to detect if samples from different humans are mixed while demiltiplexing? we have 4 samples per lane and 8 lanes in total. After demultiplexing, it turned out that some samples have double the size of other samples. The average size per sample is 10GB, but for our last run, what ...
human samples ngs wes demultiplex bam written 10 weeks ago by lait80
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low coverage & BAF plots have three peaks
... our last sequencing run (WES, ILLUMINA) gave us low coverage for our samples (still we do not know why!). When I tried to produce the density for the b-allele frequency (calculated from the vcf files), the plots appeared to have three peaks instead of one. What could be the explanation for this? an ...
b-allele frequency low coverage wes human samples written 10 weeks ago by lait80
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Comment: C: Workshop: Metagenomics, Metatranscriptomics, and multi'omics for microbial commu
... seems very interesting, unfortunately that coincides exactly with NGS'18. would this workshop be repeated again anytime this year? ...
written 3 months ago by lait80
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Comment: C: how to distinguish mosaicism out of germline de novo mutations
... I am just curious to know, do you mean that your mosaic variant was present in a cell with ploidy = 5 ? was it a cancer cell ? ...
written 3 months ago by lait80

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