User: archie

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archie100
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India
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Posts by archie

<prev • 93 results • page 1 of 10 • next >
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Error running gene expression based ProTINA
... Hello everyone I am using github.com/CABSEL/ProTINA/tree/master/protina_R package in order to identify protein target from time series data gene expression data. In the background, it uses Protein-Gene interaction information. I installed all required libraries such as glmnet in order to run this t ...
protina time series gene expression written 12 days ago by archie100
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Selection of SNPs after imputation
... Hello everyone I am first time working on imputation of GWAS data. I have chromosome specific VCF files. In one of the chromosome file, I have 195276 SNPs with 293 individuals. These are the steps I followed 1) Upload of VCF on Michigan imputation server with selection of reference panel All ...
gwas imputation written 3 months ago by archie100 • updated 3 months ago by Yean120
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GetPileupSummaries for each chromosome
... Hello everyone I am using GATK Mutect2 to identify somatic SNPs. I followed procedure as given in the link https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest . Here, one of the steps is to run GetPileupSummaries to summarize, read s ...
gatk written 4 months ago by archie100
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Comment: C: minimum reads for the splicing event analysis ?
... Thanks lieven for quick response. I am talking about short reads from RNA-Seq data. As there are different ways to perform the splicing: reference based and denovo based. I managed to get paired end RNASeq data with 44.3 million reads (QC filtered) per sample. Can I use it for discovery of comm ...
written 5 months ago by archie100
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minimum reads for the splicing event analysis ?
... Hello I am working on human genome. It is always recommended to choose sequencing depth based on the experimentation purpose . In my project, I need to estimate isoform expression (Ψ values, for “Percent Spliced In” or “Percent Spliced Isoform”) and to identify the splicing events between multi ...
isoform expression alternative splicing written 5 months ago by archie100 • updated 5 months ago by lieven.sterck9.1k
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include vcf header
... I used vscan2vcf.py to convert somatic text (from varscan) output to vcf output by software available at https://github.com/student-t/Varscan2VCF Input look like : chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somat ...
varscan written 10 months ago by archie100
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TCGA data , filtration and normalization
... I downloaded data using TCGA2STAT across two omics profiles using following code. library(TCGA2STAT) seq <- getTCGA(disease="OV", data.type="RNASeq2") met <- getTCGA(disease="OV", data.type="Methylation", type="all") seq.met <- OMICSBind(dat1 = seq$dat, dat2 = met$dat) str(seq.met) 1) ...
omics tcga genomics normalization written 10 months ago by archie100
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TCGA array expression and rnaseq expression batch correction
... Hi everyone In one of the article mentioned " Before starting the PDAC data analysis we first checked for possible batch effect in different types of data using Mbatch ". (Mishra et al 2019) here different data types refers to methylation, expression. 2) I found another script where batch effect ...
rnaseq tcga expression written 14 months ago by archie100
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Multi samples (Normal and Tumor) somatic SNPs identification
... Hi everyone I have bam files of multiples normal and tumor samples. For the efficient SNPs prediction, Its recommended to have merged multi sample vcf file. These are steps I followed 1. Mapping of all T and N samples to get multi samples bam file ( Tumor 20 Bam files : Normal 20 Bam files) 2. ...
vcf gatk snp mutlisamplevcf whole-exom written 15 months ago by archie100
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multi sample vcf to data matrix
... Hi everyone I have almost 50 VCF files consisting of information of somatic and germline SNPs. I need to convert this data from vcf to matrix format as given below : sample1 samples2 Gene1 0 1 Gene2 1 0 Gene3 1 ...
vcf gatk snp written 15 months ago by archie100 • updated 15 months ago by ATpoint42k

Latest awards to archie

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 10 weeks ago, created a question with more than 1,000 views. For input format file for DiscoSNP software run
Popular Question 4 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 5 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 5 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 5 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 6 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 10 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 10 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 11 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 12 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 14 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 16 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 16 months ago, created a question with more than 1,000 views. For Markduplicates in RNASEQ
Popular Question 16 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 17 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 20 months ago, created a question with more than 1,000 views. For rRNA in human
Scholar 21 months ago, created an answer that has been accepted. For C: Error of Netics : Multi omics intergration tool
Popular Question 23 months ago, created a question with more than 1,000 views. For rRNA in human

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