User: J.F.Jiang

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J.F.Jiang800
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800
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Location:
China
Last seen:
1 month ago
Joined:
8 years, 10 months ago
Email:
a************@gmail.com

Posts by J.F.Jiang

<prev • 248 results • page 1 of 25 • next >
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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 8 weeks ago by J.F.Jiang800 • updated 25 days ago by Kevin Blighe56k
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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 3 months ago by J.F.Jiang800
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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 3 months ago by J.F.Jiang800 • updated 12 weeks 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 5 months ago by J.F.Jiang800
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Comment: A: CNV analysis for tumor panel
... the input data is target sequencing using IDT Capture probe. ...
written 8 months ago by J.F.Jiang800
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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 8 months ago by J.F.Jiang800 • updated 8 months ago by Eric T.2.6k
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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 19 months ago by J.F.Jiang800
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Comment: C: remove primer sequences from BAM file
... yes, -L option can handle with non-overlapped regions. ...
written 19 months ago by J.F.Jiang800
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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 19 months ago by J.F.Jiang800 • updated 19 months ago by WouterDeCoster43k
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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 19 months ago by J.F.Jiang800 • updated 11 weeks ago by hongen.hugo.xu0

Latest awards to J.F.Jiang

Great Question 3 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 4 months ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 7 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
Popular Question 19 months ago, created a question with more than 1,000 views. For database of genetic alternations for inherited cancer
Appreciated 19 months ago, created a post with more than 5 votes. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Epic Question 19 months ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
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 getting haplotype and diplotype information from a batch of WGS data
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 homozygous primer for PCR
Good Question 19 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 19 months ago, created a question with more than 1,000 views. For primer design using BLASTn
Popular Question 19 months ago, created a question with more than 1,000 views. For power analysis for sample counts based on MAF
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 22 months ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Student 22 months ago, asked a question with at least 3 up-votes. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 22 months ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 22 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 variant calling based on ab1 file from Sanger sequencing
Popular Question 2.2 years ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 2.2 years ago, created a question with more than 1,000 views. For database of genetic alternations for inherited cancer
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
Great Question 2.2 years ago, created a question with more than 5,000 views. For disadvantage of NextSeq 500 compared with MiSeq
Great Question 2.2 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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