User: J.F.Jiang

gravatar for J.F.Jiang
J.F.Jiang850
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850
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China
Last seen:
1 week, 3 days ago
Joined:
9 years, 5 months ago
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a************@gmail.com

Posts by J.F.Jiang

<prev • 256 results • page 1 of 26 • next >
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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 8 weeks ago by J.F.Jiang850
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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 11 weeks ago by J.F.Jiang850
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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 11 weeks ago by J.F.Jiang850 • updated 11 weeks ago by d-cameron2.2k
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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 5 months ago by J.F.Jiang850
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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 6 months ago by J.F.Jiang850
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Comment: C: fusion detection for DNA Sequencing data
... will have a try, and response if have any question ...
written 6 months ago by J.F.Jiang850
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fusion detection for DNA Sequencing data
... Hi all, We have designed IDT probe to enrich the target region for tumor samples, including intron regions of known fusion genes. We have tried several fusion detection tools, such as delly, manta, genefuse to determine the fusion status, however, we found delly and manta were sometimes lack of se ...
fusion ngs dna written 6 months ago by J.F.Jiang850 • updated 6 months ago by d-cameron2.2k
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Comment: C: CNV analysis for tumor panel
... Thanks, I tried both FREEC and CNVKit. Both work well, but sometimes came with some bugs, especially depth calculation of FREEC. ...
written 6 months ago by J.F.Jiang850
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looking somatic variants interpreter, AS CKB database
... Hi, After calling somatic variants from tumor samples against normal ones, we still get a lot of true somatic variants that require variants-drug interpretations. CKB database offers lots of high level annotations, as well as those pre-clinic ones, which can largely provide comprehensive actionabl ...
somatic ckb interpreter written 9 months ago by J.F.Jiang850 • updated 7 months ago by Kevin Blighe66k
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Comment: C: convenient tools to collect target mapping metrics
... I've tried PICARD to get the HSMetrics from bam file. However, it is very interesting that it filter those reads not uniq mapped to the target, as PF_BASES_ALIGNED. However, ON_BAIT_BASES and ON_TARGET_BASES are quite different, although same interval file is offered. For example, 90% bases are un ...
written 10 months ago by J.F.Jiang850

Latest awards to J.F.Jiang

Epic Question 5 weeks ago, created a question with more than 10,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
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Epic Question 6 weeks ago, created a question with more than 10,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 4 months ago, created a question with more than 1,000 views. For primer trimming tools
Student 4 months ago, asked a question with at least 3 up-votes. For How Can I Obtain All Snp Rs#?
Popular Question 4 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 5 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
Popular Question 6 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 10 months ago, created a question with more than 5,000 views. For Obtain The Gene Level Cnv Matrix From Tcga Level3 Cnv Data
Popular Question 11 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 14 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
Epic Question 2.2 years ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Good Question 2.2 years ago, asked a question that was upvoted at least 5 times. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For power analysis for sample counts based on MAF
Popular Question 2.2 years ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Popular Question 2.5 years ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 2.5 years ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data

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