User: badredda

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badredda40
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Posts by badredda

<prev • 12 results • page 1 of 2 • next >
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Answer: A: TCGA calling pipeline query
... Hey again, Back to your question: > Can anyone please explain how the TCGA browser calculates mutation rates? The Gene/Mutation data for these exploration visualizations comes from the Open-Access MAF files on the GDC Portal. If you take the union of the mutations in this file you should come ...
written 5 weeks ago by badredda40
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Comment: C: TCGA calling pipeline query
... Hi there, Do you mind if I ask how you performed the combining of the four files ? And the TP53 mutation rate ? I think this is a good question. It is important to understand first what does the Exploration says: - **# Affected cases in cohort**: Breakdown of affected cases in cohort. Number of ...
written 5 weeks ago by badredda40
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Answer: A: Overlap of variants between CaVEMan and MuTect2 ?
... Sorry to bump, I am still awaiting more opinions from people on this topic. Thanks ! ...
written 5 weeks ago by badredda40
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Comment: C: Overlap of variants between CaVEMan and MuTect2 ?
... Thank you for your feedback dariober. I will get back to you soon with news concerning the venn diagrams. I plan to take the overlapped variants and perform an annotation to see if the same genes are impacted. Edit: It wouldn't really mean too much to compare actually the mutated genes. Do you hav ...
written 6 weeks ago by badredda40
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Overlap of variants between CaVEMan and MuTect2 ?
... Hello everyone, I want to discuss with Biostars community and the specialists on Exome-seq the two known callers: [MuTect2][1] and [CaVEMan][2]. As far as I know, there hasn't been any papers when comparing both tools but I heard people claiming that the overlap goes to at least 80%. In my analysis ...
whole exome sequencing mutect2 caveman sequencing written 6 weeks ago by badredda40
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Comment: C: [solved] SnpEff reports intron variants in exons ?
... @Kevin Blighe Thank you for the explanation. I will take your opinion into consideration next time. @fin swimmer Thank you for your help. Actually, that variant coming in the blue bar of GRCh37.75 was an intron. I am laughing at myself now for misunderstanding :)) Everything's cleared. Thanks again ...
written 7 months ago by badredda40
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Comment: C: SnpEff reports intron variants in exons ?
... Now I am a bit confused. I expected it to be exonic because the variant comes within the exon as shown in IGV when its being annotated with GRCh37.75. I followed your link to ensembl and indeed it does show it being an intron or downstream intron. Is it me misinterpreting the representation of the g ...
written 7 months ago by badredda40
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Comment: C: SnpEff reports intron variants in exons ?
... Hello finswimmer, yes, here's the line of the variant shown above in the IGV for GRCh37.75: chr1 1573078 rs201088964 A G . alt_allele_in_normal;panel_of_normals DB;ECNT=1;HCNT=12;MAX_ED=.;MIN_ED=.;NLOD=7.46;TLOD=8.02;ANN=G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST ...
written 7 months ago by badredda40
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[solved] SnpEff reports intron variants in exons ?
... Dear community, I am working on produced VCF files from whole exome sequencing prostate cancer patients using MuTect2. I have compared normal/tumor matched samples and found mutations. During library preparation, we used a kit for exome capture (SureSelect Human All Exon V6). Next, I wanted to perf ...
annotation snpeff exome-seq snp written 7 months ago by badredda40 • updated 7 months ago by cpad01125.2k
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CHASM vs VEST
... Hello dear Biostars community, I would like to use CRAVAT(https://www.cravat.us/) tools VEST and CHASM for somatic functional annotation but I can't figure out the difference between the two tools. Both of the tools uses a machine learning method and I know that VEST include also indels (which CHAS ...
chasm vest cravat functional somatic annotation written 8 months ago by badredda40

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