User: A

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Posts by A

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Comment: C: GISTIC 2.0 all threshold file versus genome browser
... Sorry @Kevin Blighe does makes any difference if instead of `Segment_Mean = log2(tumour copy number / 2)` I use `Segment_Mean = log2(tumour copy number / average ploidy of each sample)` ...
written 8 hours ago by A3.7k
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(Closed) The number of axons in a segment
... Hi How I can get how many exons are in a genomes range like below > head(df) Chromosome Start End 1 64613 5707515 ...
exome genomicsrange R written 1 day ago by A3.7k
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Comment: C: Alternative allele in VEP output
... Thank you In this link there is a sample data and script to calculate recombinant homologous deficiency from SNVs https://bitbucket.org/msecrier/analysisscripts.secrier_etal.natgen2013/src/master/DDR.scripts/sampleData/ I don't know from where Maria has obtained such a VEP because VEP did not giv ...
written 3 days ago by A3.7k
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Comment: C: Alternative allele in VEP output
... Thank you I have annotated my .vcf by web VEP and this is output.vep head(my_VEP) #Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra . 1:782112-782112 A ENSG00000237491 ENST00 ...
written 3 days ago by A3.7k
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Comment: C: Alternative allele in VEP output
... Thank you, so if I need both alternative and wild alleles in one file I should add the wild allele manually? ...
written 4 days ago by A3.7k
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Alternative allele in VEP output
... Hi I have annotated a vcd file by online VEP I am trying were the alternative allele is in the vet output > head(VEP) #Uploaded_variation Location Allele Gene Feature 1: . 1:782112-782112 A ENSG00000237491 ENST00000412115.2 ...
vcf wgs vep written 4 days ago by A3.7k • updated 4 days ago by Ben_Ensembl1.3k
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Comment: C: An individual gene in different peak of GISTIC
... I see, thank you so much ...
written 7 days ago by A3.7k
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Comment: C: An individual gene in different peak of GISTIC
... Sorry @Kevin Blighe to be too rude in questioning By your tutorial I mapped gene symbols to genomic aberration regions and I have some thing like below SampleID Chromosome Start End Total_CN Minor_CN Plodidy GeneSymbol Chr Start End LP6005500-DNA_D03 1 10583 5726928 2 0 2.663336 DDX11L1 1 ...
written 7 days ago by A3.7k
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Comment: C: An individual gene in different peak of GISTIC
... Thank you At some point yes this post is related to that link Here my concern was a gene in different peaks and there non agreement of WGS and RNAseq with biology concept ...
written 7 days ago by A3.7k
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Comment: C: An individual gene in different peak of GISTIC
... Actually I have prepared GISTIC input like markers file and segmentation by a script they sent to me The only thing may differ is -ta and -td threshold for GISTIC This is more and a month I'm trying different threshold but again I'm seeing non agreement For instance I'm seeing amplification of an ...
written 7 days ago by A3.7k

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
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