User: genetic

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genetic40
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40
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United States
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1 year, 2 months ago
Joined:
4 years, 10 months ago
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Posts by genetic

<prev • 14 results • page 1 of 2 • next >
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Barcoding for cfDNA?
... Hello, We will use barcoding system for cfDNA WES (both cancer and normal). In addition to cfDNA WES, we will perform tissue WES (same patients). My question is, if we do barcoding system for cfDNA WES, should we use barcoding system for tissue WES? Thank you in advance. ...
cfdna barcoding sequencing written 15 months ago by genetic40 • updated 15 months ago by genomax72k
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cfDNA target seq vs. cfDNA WES
... Hello, We have done cfDNA target seq. for 60 samples (cancer, 5000x, ~80 gene panel). We are about to confirm our findings from cfDNA using tissue samples from same patients (either target seq. or WES). However, due to our budget, we have to choose one option --> either tissue target seq. or tis ...
cfdna forum written 15 months ago by genetic40
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Comment: C: R programming question
... I need this code for my NGS data. We have whole exome sequencing data, and need to transform to interpret them. Thank you. ...
written 15 months ago by genetic40
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Comment: C: R programming question
... > head(input) V1 V2 V3 V4 V5 V6 1 A 1 2 3 4 5 2 B 1 2 NA NA NA 3 C 3 5 NA NA NA 4 D 3 NA NA NA NA 5 E 4 5 6 1 8 ...
written 15 months ago by genetic40
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GATK hg19 bundle question
... I've downloaded GATK hg19 bundle datasets. Can I use 1000G_phase1.indels.hg19.sites.vcf instead of 1000G_phase1.indels.hg19.vcf? What is difference between these 2 files? 1000G_phase1.indels.hg19.vcf 1000G_phase1.indels.hg19.sites.vcf Mills_and_1000G_gold_standard.indels.hg19.vcf Mills_and_1000 ...
gatk written 2.0 years ago by genetic40 • updated 24 months ago by Biostar ♦♦ 20
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Comment: C: picard installation failure
... Thank you. It works. ...
written 2.0 years ago by genetic40
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Answer: A: picard installation failure
... Hello, I've invoke it with java, but I still have an error. Could you please let me know how should I fix this? Thank you. [root@NGS:han]# java -jar picard.jar Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52. ...
written 2.0 years ago by genetic40
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(SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
... Hello, I am working on functional annotation of my exome-chip variants. I am not sure what are the differences using annotation from (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE). ANNOVARannotates all SNPs using refseq's sequence information without using any algorithm. (SIFT, Polyphen, P ...
genome gene snp written 3.7 years ago by genetic40 • updated 12 months ago by RamRS24k
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Phasing using SHAPEIT
... Hello, I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) analysis for recessive rare variant.. I will not perform imputation.  I am running SHAPEIT, and I see in the log file it says: Parameters :   * Seed : 1442251531   * Parallelisation: 12 threads   * Ref a ...
assembly sequence snp alignment sequencing written 4.1 years ago by genetic40
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Comment: C: PLINK results interpretation
... Yes. you guys are right. There are some samples which contain missing genotypes. Thank you! ...
written 4.2 years ago by genetic40

Latest awards to genetic

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Phasing using SHAPEIT
Popular Question 3.6 years ago, created a question with more than 1,000 views. For What is the difference between fine-mapping and targeted sequencing?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to convert vcf dosage file format to mldose format?

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