User: J.F.Jiang

gravatar for J.F.Jiang
J.F.Jiang750
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750
Status:
Trusted
Location:
China
Last seen:
6 days ago
Joined:
8 years, 2 months ago
Email:
a************@gmail.com

Posts by J.F.Jiang

<prev • 244 results • page 1 of 25 • next >
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Comment: A: CNV analysis for tumor panel
... the input data is target sequencing using IDT Capture probe. ...
written 28 days ago by J.F.Jiang750
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CNV analysis for tumor panel
... Hi all, In order to evaluate the drug response of patient, we want to analyze the CNV status of target region. The panel was developed and synthetized by IDT. I am wondering if there is any tool to define the CNV status of the target region, such as MET/EGFR/HER2, beside GATK, FREEC, XHMM, since ...
cnv written 29 days ago by J.F.Jiang750 • updated 21 days ago by Eric T.2.5k
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Comment: C: Free Genetic Genealogy Software
... yhaplo use isogg 2016 as the reference. Updating to 2018 is quite confusing for me. Is there any solution or other similar tool? ...
written 12 months ago by J.F.Jiang750
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Comment: C: remove primer sequences from BAM file
... yes, -L option can handle with non-overlapped regions. ...
written 12 months ago by J.F.Jiang750
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Comment: C: remove primer sequences from BAM file
... ------->--------*-------------------------------<------------- ------------>--------------------<----------------------- Take the scenario above as consideration, if position * is always T, but C in the primer region of the second amplicon. The calling result wil ...
written 12 months ago by J.F.Jiang750 • updated 12 months ago by WouterDeCoster40k
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remove primer sequences from BAM file
... Hi all, I am dealing with amplicon data, which was obtained from multiplex PCR. Original primers can largely increase the mapping accuracy, since some amplicons are highly homologous with little difference within primer region. And since these primers may introduce FAKE SNPs when they are within ...
bam primer written 12 months ago by J.F.Jiang750
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autosomal ancestry inference
... Hi all, I am very interested in ancestry inference. 1. autosomal ancestry I've followed the tutorial from https://github.com/pcgoddard/Burchardlab_Tutorials/wiki/ADMIXTURE#popfile. However, decision on cluster information K is quite confusing. For example, there are already 12 populations among ...
gwas ancestry written 12 months ago by J.F.Jiang750 • updated 12 months ago by Kevin Blighe46k
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Simulate genotypes for SNPs, considering MAF and LD structure
... Hi all, I want to simulate genotypes of several SNPs for 10,000 samples. A Bernoulli sampling is applied to generate SNP genotypes (0/0, 0/1, 1/1) for random samples. However, this will not consier the LD structure among thse SNPs, which was obtained from 1KG dataset. Is there any tools of Gith ...
maf simulation snp genotype ld written 19 months ago by J.F.Jiang750 • updated 9 months ago by zx87547.9k
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Comment: C: extract region bam
... Thanks, Either seal.sh or cutprimers.sh is spliting the raw sequencing file based on matched primers. However, I still want to begin from bam file. ...
written 20 months ago by J.F.Jiang750
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extract region bam
... Hi all, I want to extract bam of specific amplicon to evaluate the according amplicon performance. I used to use samtools view xx.bam chr:start-end to extract the bam, however, if the two amplicon are totally overlapped, this command will return us the whole reads covering the two region. For exam ...
region bam written 20 months ago by J.F.Jiang750 • updated 20 months ago by h.mon26k

Latest awards to J.F.Jiang

Popular Question 11 months ago, created a question with more than 1,000 views. For homozygous primer for PCR
Epic Question 11 months ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
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Popular Question 11 months ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 11 months ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 11 months ago, created a question with more than 1,000 views. For database of genetic alternations for inherited cancer
Good Question 11 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 11 months ago, created a question with more than 1,000 views. For primer design using BLASTn
Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For power analysis for sample counts based on MAF
Appreciated 11 months ago, created a post with more than 5 votes. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Popular Question 15 months ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 15 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Student 15 months ago, asked a question with at least 3 up-votes. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Great Question 15 months ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 15 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Popular Question 19 months ago, created a question with more than 1,000 views. For fastest method to get potential amplicons based on paired-primers
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Scale The Expression Data Of Affy To A Same Average Intensity
Popular Question 19 months ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 19 months ago, created a question with more than 1,000 views. For database of genetic alternations for inherited cancer
Popular Question 19 months ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 19 months ago, created a question with more than 1,000 views. For Genetic rsisk score, polygenic risk score
Popular Question 19 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 19 months ago, created a question with more than 5,000 views. For disadvantage of NextSeq 500 compared with MiSeq
Great Question 19 months 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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