User: Defne

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Defne0
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Posts by Defne

<prev • 6 results • page 1 of 1 • next >
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Comment: C: How to subset a set of variations from a VCF on specific chromosome and between
... Its huge number of variations ignored (I have file with 800 samples and i want to search the variations for all the samples in this region). The command generates only some of variation and just once ( for exemple, if a variation appears in 5 samples, i want to find 5 lines with this variation in th ...
written 4 days ago by Defne0
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Comment: A: How to subset a set of variations from a VCF on specific chromosome and between
... Thank u for help! I used the command of bcftools after indexing the vcf file. my command line looks like this: bcftools view file1.vcf.gz "chr9:81583683-81689305" -O v file2.vcf. It works but it doesn't return all the variations that i want to get, just some of them while I want to get all the ...
written 4 days ago by Defne0
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How to subset a set of variations from a VCF on specific chromosome and between 2 postions?
... Hi, I'm a very beginner on using bash so my question may seem stupid for some of you. I have a VCF annotated file with a big number of samples. I want to subset a file from this one with all the variations of a gene (located on the chromosome ($1 = chr9) and between the position ($2 = POS) 815836 ...
vcf subset awk bash written 12 days ago by Defne0
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DB or Tool searching for miRNA validated targets in cancer?
... Hi all, I have a list of miRNA and i want to know its validated target in a cancer and the pathways in which implicated. I used miRTarBase and i know there is many web servers but I want to know if there an R package or a tool not complicated (for beginner) to find miRNA validated tagets and recentl ...
targets pathways mirna validated targets cancer written 9 months ago by Defne0 • updated 9 months ago by poyarkov.stanislav40
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Comment: A: Searching for mutation
... Hello, For Example, for IDH1, we found the mutations R132H or R132S and many other mutations... So i want a tool that give me the names of all the mutations of IDH1 (for example) and their positions or the variants that were described with their identifier ...
written 10 months ago by Defne0
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Searching for mutation
... Hello, I have a gene and i want to get a list of all the mutations and variants that were described until now for this gene in cancer (or the proteine because i have some AA mutations for the proteine). I used cosmic but i want other tool or R package more reliable because i'll do the same work wi ...
gene R mutation variant snp written 10 months ago by Defne0

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