User: Tania

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Tania50
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Posts by Tania

<prev • 86 results • page 1 of 9 • next >
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Can we omit the normal input and compare tumor to pon only in MuTect2?
... Hi Everyone If we don't have normal-tumor matched sample. Is it reasonable to run tumor against PON with no nomral input. Like I want to compare the Tumor to the PON not to specific normal sample. Like this, with no normal input (`-I:normal`) just the tumor sample and the PON java -jar ...
tumor rna-seq mutect written 19 hours ago by Tania50
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Comment: C: CosmicCodingMuts.vcf.gz for hg38?
... Thanks erwan.scaon :) ...
written 13 days ago by Tania50
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Comment: C: CosmicCodingMuts.vcf.gz for hg38?
... Thanks dariober, I already downloaded the file, converting the chr 1 thing is what I wanted, will try the code now. Very much appreciated. ...
written 13 days ago by Tania50
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CosmicCodingMuts.vcf.gz for hg38?
... Hi all I downloaded `CosmicCodingMuts.vcf.gz` from Cosmic site. Then I use for my RNAseq somatic calling `Homo_sapiens_assembly38.dbsnp138.vcf` from GATK resource bundle. And also use reference: `Homo_sapiens_assembly38.fasta` **Where I can find Cosmic files with `chr` contigs for hg38?** ...
somaticmutations rna-seq written 13 days ago by Tania50 • updated 13 days ago by dariober8.6k
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How can we find the list of genes involved in each pathway using Gage?
... Hi all If we detected the pathways using gage, how can I find the list of genes involved in each pathway? I mean how to output the genes enriched significanlty in each pathway that was in my list of genes? res$symbol <- mapIds(org.Hs.eg.db, keys=row.names( ...
pathways rna-seq gage written 26 days ago by Tania50
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Low frequent variants in SINE regions?
... **Hello every one** If we have a low frequent variant `(GT:GQ:DP:VF:GQX:PL:AD ==> 0/1:99:910:0.095:99:549,0,17114:824,86)` (related to my previous post). and it is from DNA blood samples and I found the variant belongs in the **SINE** region. We won't be surprised if the individual is found ...
sine region variants written 4 weeks ago by Tania50
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Comment: C: Interpretation for lowfrevariant
... Hi Kevin, How can I know if it mosaicism or not? We have an individual with a very rare phenotype, what else we can check to decide? I don't have any more information about him, but could ask. But what information I should relate to this? ...
written 5 weeks ago by Tania50
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Comment: C: Interpretation for lowfrevariant
... Thanks WouterDeCoster and Titus so much. ...
written 5 weeks ago by Tania50
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Comment: C: Interpretation for lowfrevariant
... I don't know about the region, how do we know? it is: G -> A AC=42;AF=0.5;AN=80;DP=27355;EXON;FC=Missense_V425I;GI=SUCLG2;QD=17.62;SF=2,3,9,13,16,17,19,24,26,27,28,30,33,43,44,49,75,86,89,91,93,96,100,101,102,104,105,113,114,117,123,124,127,129,131,132,133,134,135,137;TI=NM_001177599 and 0/1: ...
written 5 weeks ago by Tania50
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Interpretation for lowfrevariant
... Hi every one If we have this variant: GT:GQ:DP:VF:GQX:PL:AD ==> 0/1:99:910:0.095:99:549,0,17114:824,86 And it did not `pass`, it is reported as `LowVariantFreq` I understand that this is because AD =824,86. which means we have 824 reads support the ref and 86 only support the alt. Bu ...
vcf written 5 weeks ago by Tania50

Latest awards to Tania

Supporter 9 weeks ago, voted at least 25 times.
Rising Star 9 weeks ago, created 50 posts within first three months of joining.

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