User: J.F.Jiang

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J.F.Jiang860
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860
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China
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3 days, 9 hours ago
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9 years, 9 months ago
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Posts by J.F.Jiang

<prev • 261 results • page 1 of 27 • next >
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genomewide CNV analysis and plot from low pass WGS data
... Hi all, We are using lpWGS data to analyzed the CNV status of the genome, and plot the Log2Ratio, using samples from misscarriage ones. ichorCNA was used. However, we found the CNV plot was roughly noised across the genome, which is largely different from the plot offered in the paper, although th ...
wgs cnv cnvseq written 4 weeks ago by J.F.Jiang860
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Comment: C: public tools to distinguish germline variants from somatic ones in NGS data with
... YES, it is very hard without the matched normal. Thanks for explaination. ...
written 3 months ago by J.F.Jiang860
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Comment: C: public tools to distinguish germline variants from somatic ones in NGS data with
... We indeed use gnomAD to annotate the VCF file. However, pathogenic variants are not so frequently. Even ClinVar and HGMD database are applied, it is very hard to determine those variants not existed in database. ...
written 3 months ago by J.F.Jiang860
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public tools to distinguish germline variants from somatic ones in NGS data without matched normal
... Hi all, Distinguishing germline variants, especially those pathogenic ones, are of great importance, since these variants might increase the cancer susceptibility in other family members. It is quite challenge when blood sample/matched normal is absence, leaving a lot of variants with zygosity/All ...
somatic ngs tumor germline written 3 months ago by J.F.Jiang860 • updated 9 weeks ago by Biostar ♦♦ 20
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best tool to evaluate the CNV status of germline samples using 1x WGS
... Hi all, In order to evaluate the CNV status of samples, we performed 1x WGS as CNVSeq, together with WES. However, we found hard to select the CNVseq tool using 1x WGS data, although most of them used window sliding to gather the CNV regions. Any suggestions? Thanks, Junfeng ...
wgs cnv written 4 months ago by J.F.Jiang860
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Max mutation allele frequency against tumor purity
... Hi all, We are using GATK Mutect2 to call the somatic variants from tumor samples. We found some of the variants had max allele frequency larger than 0.5, which made me quite confused. Unless the sample is quite pure (100%), the theoretical allele frequency should be less than 0.5. While sometime ...
tumor af purity written 6 months ago by J.F.Jiang860
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Comment: C: HPV EBV typing from cancer genome data
... Thanks, kraken, or other metagenomic tools, apply kmer strategy to search the virus status from the fq data. Can it do further step, such as determine the HPV alleles (hpv18)? And I will carefully review the tool, any comments and suggestions will be appreciated. ...
written 6 months ago by J.F.Jiang860
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HPV EBV typing from cancer genome data
... Hi all, We designed several probes to enrich the virus, such as hpv, ebv, hbv, from the cancer tissue DNA samples. Is there any tool that can directly typing these virus from the raw fq data? Thanks. Junfeng ...
ebv hpv ngs written 6 months ago by J.F.Jiang860 • updated 6 months ago by d-cameron2.3k
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LOH segment inferring from WES data for germline sample
... Hi all, We applied WES to determine the pathogenic variants. Meanwhile, we want to check the LOH status of the sample. We used CNVKit to calculate the CNV of the sample. I am wondering is there a tool to get the LOH segment of the samples? ...
loh wes written 9 months ago by J.F.Jiang860
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Comment: C: fusion detection for DNA Sequencing data
... Hi Kevin, Any suggestions for the input bam? Since unproper mapped reads might be removed during alignment, what kind of bam file should I used? I tried raw data mapped file or markdup one, without any result, while delly or manta can give out. ...
written 10 months ago by J.F.Jiang860

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