User: J.F.Jiang

gravatar for J.F.Jiang
J.F.Jiang650
Reputation:
650
Status:
Trusted
Location:
China
Last seen:
12 hours ago
Joined:
6 years, 6 months ago
Email:
a************@gmail.com

Posts by J.F.Jiang

<prev • 236 results • page 1 of 24 • next >
0
votes
1
answer
105
views
1
answers
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 12 hours ago by J.F.Jiang650
0
votes
1
answer
105
views
1
answer
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 4 days ago by J.F.Jiang650 • updated 1 day ago by h.mon9.6k
0
votes
0
answers
84
views
0
answers
Comment: C: pairwise calculation of relationship based on selected SNPs with MAF>0.3
... I can definitely use vcftools or directly use PLINK to convert vcf to ped, and then use PLINK to calculate IBD. However, genotypes of the samples were saved into database. If I am calculating the pairwise IBD for new 1000 samples against the database. I need to extract the genotypes from database, ...
written 4 days ago by J.F.Jiang650
0
votes
0
answers
84
views
0
answers
pairwise calculation of relationship based on selected SNPs with MAF>0.3
... Hi all, We are genotyping ~2000 SNP in a Panel using NGS method. We want to build a metrics to calculate the relationship for one sample against all in our database, in order to avoid taking wrong samples that are already existed in our lab. I used to use PLINK to calculate IBD score for GWAS dat ...
relationship snp written 13 days ago by J.F.Jiang650
0
votes
1
answer
155
views
1
answers
Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... Actually I also found such a strange issue, when -nct was applied for WGS or WES data, it significantly decrease the runing time, but not for data sequenced from amplicons. ...
written 21 days ago by J.F.Jiang650
0
votes
0
answers
159
views
0
answers
Comment: C: Fasted method to genotype given SNPs from NGS data
... I did add -L snp.bed as the calling restriction, but the runing time did not decrease a lot even using the snp.vcf as the restriction region. ...
written 21 days ago by J.F.Jiang650
0
votes
0
answers
159
views
0
answers
Fasted method to genotype given SNPs from NGS data
... Hi all, We are focusing on 3000 known SNPs. Instead of genotype these SNPs from array or taqman, we use PCR to enrich these SNPs, and get them sequenced on HiSeq. We found genotype these 3000 SNPs cost lots of time. We split the 3000 SNPs into two categories, 1000 of them were called by GATK Un ...
ngs genotype snp written 21 days ago by J.F.Jiang650
0
votes
1
answer
155
views
1
answers
Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... -nt can be only applied in UnifiedGenotyper. Split bam against reference is a kind of simple methods for distributed computation, as bcbio-ngs did. Any other methods? ...
written 21 days ago by J.F.Jiang650
0
votes
1
answer
155
views
1
answer
GATK HaolotypeCaller takes too much time for variant calling
... Hi all, I am using GATK HaplotypeCaller to genotype ~3000 SNPs from amplicon sequencing data, using --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles $vcf --output_mode EMIT_ALL_SITES mode. Howver, it take huge time to call these variants, ~20h. And I found that adding -nct option did not work, ...
haplotypecaller gatk long written 21 days ago by J.F.Jiang650 • updated 21 days ago by bluemonster080830
0
votes
0
answers
148
views
0
answers
get CDS cordinates for genes, excluding UTR
... Hi all, I want to collect the gene exon cordinates information for GATK variant calling usage. As far as I know, UCSC can offer me the great utility to extract the information. Howver, it can only extract exon only or UTR only. Although I can write a script to get those cordinates and find the r ...
gene cds written 21 days ago by J.F.Jiang650

Latest awards to J.F.Jiang

Popular Question 20 days ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 8 weeks ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 10 weeks ago, created a question with more than 1,000 views. For primer trimming tools
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Genetic rsisk score, polygenic risk score
Popular Question 12 weeks ago, created a question with more than 1,000 views. For primer trimming tools
Great Question 4 months ago, created a question with more than 5,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Epic Question 7 months ago, created a question with more than 10,000 views. For How To Plot Clustered Mutation Profiles Using Tcga Mutation Data
Popular Question 7 months ago, created a question with more than 1,000 views. For Calculating Rpkm From Rsem Using Tcga Rnaseqv2 Level3 Data
Popular Question 7 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 7 months ago, created a question with more than 1,000 views. For primer design function for perl program
Popular Question 7 months ago, created a question with more than 1,000 views. For primer trimming tools
Epic Question 7 months ago, created a question with more than 10,000 views. For Database For Transcription Factor Binding Sites Annotation (Tfbs)
Epic Question 9 months ago, created a question with more than 10,000 views. For Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Epic Question 9 months ago, created a question with more than 10,000 views. For Database For Transcription Factor Binding Sites Annotation (Tfbs)
Epic Question 9 months ago, created a question with more than 10,000 views. For Plotting A Pie-Chart Of Molecular Function Using Gene Ontology Method?
Popular Question 9 months ago, created a question with more than 1,000 views. For Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Great Question 9 months ago, created a question with more than 5,000 views. For Database For Transcription Factor Binding Sites Annotation (Tfbs)
Popular Question 9 months ago, created a question with more than 1,000 views. For Datasets Downloads From Eqtl.Uchicago.Edu
Popular Question 9 months ago, created a question with more than 1,000 views. For Mirna Or Tf Enrichment, Onlinedatabase? Webserver? Local Database?
Popular Question 9 months ago, created a question with more than 1,000 views. For Convert Fdr Control Q-Value To P-Value
Popular Question 9 months ago, created a question with more than 1,000 views. For Database For Transcription Factor Binding Sites Annotation (Tfbs)
Popular Question 9 months ago, created a question with more than 1,000 views. For Convert Fdr Control Q-Value To P-Value
Great Question 10 months ago, created a question with more than 5,000 views. For Database For Transcription Factor Binding Sites Annotation (Tfbs)
Great Question 10 months ago, created a question with more than 5,000 views. For Rnaseq Fpkm Quantile Normalization
Popular Question 14 months ago, created a question with more than 1,000 views. For Convert Fdr Control Q-Value To P-Value

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1517 users visited in the last hour