User: J.F.Jiang

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J.F.Jiang830
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830
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Location:
China
Last seen:
2 months ago
Joined:
9 years, 2 months ago
Email:
a************@gmail.com

Posts by J.F.Jiang

<prev • 253 results • page 1 of 26 • next >
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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 11 weeks ago by J.F.Jiang830
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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 4 months ago by J.F.Jiang830
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Comment: C: fusion detection for DNA Sequencing data
... will have a try, and response if have any question ...
written 4 months ago by J.F.Jiang830
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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 4 months ago by J.F.Jiang830 • updated 4 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 4 months ago by J.F.Jiang830
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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 6 months ago by J.F.Jiang830 • updated 5 months ago by Kevin Blighe63k
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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 8 months ago by J.F.Jiang830
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convenient tools to collect target mapping metrics
... Hi all, I want to collect some metrics for my NGS panel. To evaluate the capture efficiency of the probes, I want to calculate the on target rate from reads and base. For reads, bedtools is applied to get the rate, however, reads can be calculate twice if they span two probes. Any method to avoid ...
mapping target written 8 months ago by J.F.Jiang830 • updated 7 months ago by Biostar ♦♦ 20
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calculate MSI STATUS using predefined MSI loci
... Hi all, I've designed 27 MSI probes to capture the reads. As suggested, I used msisensor to obtain whether the loci was stable or not. I restricted the msi site to those 27 MSI sites I designed, and used the default parameter for msi detection. /bioinfo/software/msisensor2/msisensor2 msi -M /bio ...
msi msisensor written 9 months ago by J.F.Jiang830
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Comment: A: CNV analysis for tumor panel
... the input data is target sequencing using IDT Capture probe. ...
written 12 months ago by J.F.Jiang830

Latest awards to J.F.Jiang

Great Question 10 weeks ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
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 8 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 8 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 11 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
Popular Question 23 months ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 23 months ago, created a question with more than 1,000 views. For homozygous primer for PCR
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Popular Question 23 months ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 23 months ago, created a question with more than 1,000 views. For database of genetic alternations for inherited cancer
Appreciated 23 months ago, created a post with more than 5 votes. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Popular Question 23 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Popular Question 23 months ago, created a question with more than 1,000 views. For getting haplotype and diplotype information from a batch of WGS data
Popular Question 23 months ago, created a question with more than 1,000 views. For primer design using BLASTn
Epic Question 23 months ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Popular Question 23 months 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
Great Question 2.2 years ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Student 2.2 years ago, asked a question with at least 3 up-votes. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For primer trimming tools
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 2.6 years ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 2.6 years ago, created a question with more than 5,000 views. For disadvantage of NextSeq 500 compared with MiSeq
Great Question 2.6 years ago, created a question with more than 5,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data

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