User: Arko

gravatar for Arko
Arko10
Reputation:
10
Status:
New User
Location:
US/Boston/Boston University
Last seen:
1 day ago
Joined:
6 months, 1 week ago
Email:
a*****@bu.edu

Posts by Arko

<prev • 9 results • page 1 of 1 • next >
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Querying variations from a VCF file
... I have a VCF file v4.1 and I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.) from it. If there are multiple possibilities, how would I annotate the most deleterious possibility? Apart from that, I'm trying to find the number of reads supporting the var ...
vcf bioinformatics variants mutations python written 3 days ago by Arko10 • updated 1 day ago by Emily_Ensembl16k
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Comment: C: Merging and converting multiple vcf files into a SNP array
... Tried it, but BCF tools on merge considers the NON - REF as a literal allele call instead of ignoring it and a NON-REF contributes to the genotype call. ...
written 3 months ago by Arko10
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Comment: C: Merging and converting multiple vcf files into a SNP array
... GATK doesn't allow merging of VCF and gVCF files unfortunately. My aim is to obtain a single VCF file from the entire set, ...
written 3 months ago by Arko10
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Comment: A: Merging and converting multiple vcf files into a SNP array
... All things considered, what would be the fastest way to merge GVCF files and VCF files efficiently? BCF tools is a faster alternative when compared to VCF tools but doesn't work with GVCF files. ...
written 3 months ago by Arko10
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Merging and converting multiple vcf files into a SNP array
... I have 50 .VCF files each corresponding to a patient sample and what I want to do is to merge all these files together, extract based on chromosome position / SNP ID for the Genotype information and then convert it into a 012 matrix in the most time efficient and effective way possible. VCF tools an ...
vcf python bcf R written 3 months ago by Arko10
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Liftover dbSNP IDs
... I have a list of SNPs from dbSNP build 150, I want to run a batch analysis on SIFT which uses an older build of rsid's (build 138 - if I'm not mistaken). I understand that dbSNP rsids are updated based to avoid synonymous occurrences, but could someone please clarify on how would I map the rsids t ...
assembly snp written 4 months ago by Arko10 • updated 4 months ago by Pierre Lindenbaum112k
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Comment: C: Differential Expression of a normalized RNAseq expression dataset
... A rather silly question, but from the file manifest how many of the files are required to be downloaded, as from what I see each .result file contains counts and corresponding genes apart from the annotation.txt files. There is normalized and RAW data, so if I were to download only the RAW data how ...
written 6 months ago by Arko10
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Comment: C: Differential Expression of a normalized RNAseq expression dataset
... Thanks Kevin, I shall follow up on it and let you know how it works out! ...
written 6 months ago by Arko10
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Differential Expression of a normalized RNAseq expression dataset
... I have a RNAseq expression matrix obtained from TCGA (TCGA-GBM) it's been normalized. The columns are for sample IDs and the rows are for genes. I want to do a differential expression analysis. I also have the copy number matrix for the same dataset from cbioportal but I'm not exactly sure on how to ...
glioblastoma R tcga deseq rna-seq written 6 months ago by Arko10 • updated 6 months ago by Kevin Blighe30k

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