User: Maxime

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Maxime0
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Posts by Maxime

<prev • 11 results • page 1 of 2 • next >
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Answer: A: From consensus sequence with variants to protein
... I've found this tool : http://genomics.brocku.ca/Prot2gene/index.html which does what I want, if anyone come across the same question. ...
written 13 days ago by Maxime0
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From consensus sequence with variants to protein
... Hello Biostars, I have multiple gene sequences created with https://samtools.github.io/bcftools/howtos/consensus-sequence.html for probands. I would like to analyse them at protein level, to retrieve the protein sequence from those individuals including all variants. The point is to analyse some sp ...
vcf cds aligment blast ccds written 14 days ago by Maxime0
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How does SnpEff discriminate between transcripts?
... Hi, Looking for example at this line of a VCF file : 1 155322556 . C G [...] ;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R2436P|2964|ASH1L||CODING|NM_018489.2|17|1) [...] GT:AO:DP:GQ:PL:QA:QR:RO 0/0:11:55:74:0,40,100:66:917:44 0/0:4:35:99:0,81,100:8:868:31 0/1:12:32:0:1,0,100:91:658: ...
vcf snpeff uniprot transcripts written 23 days ago by Maxime0
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How to understand and analyze allele count from dbNSFP
... Hi, I have access to multiple VCF files already annotated with SnpEff + dbNSFP and I'm looking at this info field : 1000Gp1_AC so the allele count for phase 1 of 1000G. I'm analyzing denovo variants and their effect on proteins in disease context. I have a denovo variant which give me an AC of 4 ...
vcf snp dbnsfp written 4 weeks ago by Maxime0
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Comment: C: Phasing and de novo finding from VCF file
... Hi Pierre, PossibleDeNovo from VariantAnnotator doesn't seem to work. I have a VCF containing this mutation : 12 2721137 . C T 41828.10 GT:AO:DP:GQ:QA:QR:RO 0/0:0:13:59:0:456:13 0/0:1:3:1:33:81:2 0/1:3:10:54:94:210:7 0/0:0:91:99:0:2777:91 First two are, respectively, father and mother, ...
written 6 weeks ago by Maxime0
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Comment: C: Phasing and de novo finding from VCF file
... Thank you Pierre, Would you care to explain where phasing is needed? And should I do the first step in this workflow? https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinement-workflow-for-germline-short-variants ...
written 7 weeks ago by Maxime0
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Phasing and de novo finding from VCF file
... Hello, I want to analyse missense de novo variants in context of autism spectrum disorder and I have access to already annotated (SnpEff) vcf files. Each VCF has at least a trio (father, mother, proband) and sometimes an unaffected sibling. Do I need to phase before looking for de novo? Which too ...
vcf de novo snpeff written 7 weeks ago by Maxime0 • updated 7 weeks ago by Pierre Lindenbaum129k
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Getting reports (HTML/txt) for already annotated (SnpEff) vcf files and phasing/de novo findings
... Hi Biostars, I want to analyse de novo missense variants for a hundred genes in context of ASD. I have access to already annotated vcf files by SnpEff for multiple families (trios/quad) but I haven't the summary stat report. I've filtered them with SnpSift to retain only variants included in my ge ...
vcf snpeff written 3 months ago by Maxime0
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How to go from VCF file to protein level
... Hi, I need to do some modeling at protein level in the context of ASD to analyse variants. I started from a whole exome sequencing dataset and created consensus sequences for each gene with samtools/bcftools by applying an already made VCF file. Those sequences are the sequences from the reference ...
gene genome alignment protein written 3 months ago by Maxime0
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Comment: C: Validating pipeline from FASTQ to VCF
... Hi, Thank you for your consideration, I actually though that it might be too long. Isn't there a way to make some sort of spoiler section to add information without overloading the post? ...
written 6 months ago by Maxime0

Latest awards to Maxime

Scholar 13 days ago, created an answer that has been accepted. For A: From consensus sequence with variants to protein

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