User: J.F.Jiang

gravatar for J.F.Jiang
J.F.Jiang760
Reputation:
760
Status:
Trusted
Location:
China
Last seen:
16 hours ago
Joined:
8 years, 6 months ago
Email:
a************@gmail.com

Posts by J.F.Jiang

<prev • 247 results • page 1 of 25 • next >
0
votes
0
answers
45
views
0
answers
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 days ago by J.F.Jiang760
0
votes
0
answers
45
views
0
answers
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 days ago by J.F.Jiang760
0
votes
0
answers
124
views
0
answers
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 weeks ago by J.F.Jiang760
0
votes
1
answer
177
views
1
answers
Comment: A: CNV analysis for tumor panel
... the input data is target sequencing using IDT Capture probe. ...
written 4 months ago by J.F.Jiang760
0
votes
1
answer
177
views
1
answer
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 4 months ago by J.F.Jiang760 • updated 4 months ago by Eric T.2.5k
0
votes
1
answer
1.2k
views
1
answers
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 15 months ago by J.F.Jiang760
0
votes
0
answers
711
views
0
answers
Comment: C: remove primer sequences from BAM file
... yes, -L option can handle with non-overlapped regions. ...
written 15 months ago by J.F.Jiang760
0
votes
0
answers
711
views
0
answers
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 15 months ago by J.F.Jiang760 • updated 15 months ago by WouterDeCoster42k
0
votes
0
answers
711
views
0
answers
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 15 months ago by J.F.Jiang760
0
votes
1
answer
649
views
1
answer
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 15 months ago by J.F.Jiang760 • updated 15 months ago by Kevin Blighe52k

Latest awards to J.F.Jiang

Popular Question 23 days ago, created a question with more than 1,000 views. For variant calling based on ab1 file from Sanger sequencing
Great Question 3 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
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 15 months ago, created a question with more than 1,000 views. For primer design using BLASTn
Epic Question 15 months ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Appreciated 15 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 database of genetic alternations for inherited cancer
Good Question 15 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 15 months ago, created a question with more than 1,000 views. For homozygous primer for PCR
Popular Question 15 months ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 15 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 15 months ago, created a question with more than 1,000 views. For power analysis for sample counts based on MAF
Popular Question 15 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 variant calling based on ab1 file from Sanger sequencing
Popular Question 19 months ago, created a question with more than 1,000 views. For primer trimming tools
Great Question 19 months ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Student 19 months ago, asked a question with at least 3 up-votes. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 19 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 Genetic rsisk score, polygenic risk score
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 database of genetic alternations for inherited cancer
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 variant calling based on ab1 file from Sanger sequencing
Great Question 23 months ago, created a question with more than 5,000 views. For disadvantage of NextSeq 500 compared with MiSeq
Great Question 23 months ago, created a question with more than 5,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 898 users visited in the last hour