User: Arko
Arko • 10
- 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
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... 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 ...
written 3 days ago by
Arko • 10
• updated
1 day ago by
Emily_Ensembl ♦ 16k
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... 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
Arko • 10
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... GATK doesn't allow merging of VCF and gVCF files unfortunately. My aim is to obtain a single VCF file from the entire set,
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written 3 months ago by
Arko • 10
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... 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.
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written 3 months ago by
Arko • 10
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... 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 ...
written 3 months ago by
Arko • 10
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... 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 ...
written 4 months ago by
Arko • 10
• updated
4 months ago by
Pierre Lindenbaum ♦ 112k
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... 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
Arko • 10
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... Thanks Kevin, I shall follow up on it and let you know how it works out! ...
written 6 months ago by
Arko • 10
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... 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 ...
written 6 months ago by
Arko • 10
• updated
6 months ago by
Kevin Blighe ♦ 30k
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