User: umn_bist

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umn_bist320
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Posts by umn_bist

<prev • 124 results • page 1 of 13 • next >
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Any experience using SomaticSeq for RNAseq SNV?
... I just wanted to discuss the reliability of the tool. I understand that it is a high performing variant caller but it seems that the tool was made for DNA-seq? Reason being, it uses BWA aligner as shown in this paper. However, it also uses mutation callers that work "well" for RNAseq variant calling ...
rnaseq written 2.9 years ago by umn_bist320 • updated 2.9 years ago by Istvan Albert ♦♦ 79k
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Comment: C: Bowtie memory warning
... Test sample. This is a deleted post.Test sample. This is a deleted post. ...
written 2.9 years ago by umn_bist320
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Bowtie memory warning
... I am aligning my files with bowtie 1.0.0 via our HPC. bowtie /UCSC/hg19/Sequence/BowtieIndex/genome -p 16 --chunkmbs 16 -t -m 1 -S --max ${file1:0:9}_multimap.fastq -1 ${file1} -2 ${file2} ${file3} With or without `--chunkmbs`, I still get the warning. I have tried reducing the amount of threa ...
bowtie written 2.9 years ago by umn_bist320 • updated 2.9 years ago by Istvan Albert ♦♦ 79k
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Is there a way to reformat vcf 4.2 down to 4.1?
... I've been using MuTect2 (part of GATK toolkit) to call somatic variants for my RNAseq data set. The vcf file is in 4.2 format which I'm not familiar with. Is there any advantage to using 4.2 instead if I'm annotating with snpEff/annovar and filtering with snpSift? The documentations for annotation/ ...
variant calling snpsift snpeff written 2.9 years ago by umn_bist320 • updated 2.9 years ago by harold.smith.tarheel4.3k
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TCGA Broad Institute curated variants
... I am using RNA-seq data available at TCGA to call variants and through cross-checking with the curated MAF files provided by Broad Institute, it seems that there are a couple variants that either I'm not getting and some that they're not getting. I was curious if there is available documentation th ...
broad institute tcga snv rna-seq written 2.9 years ago by umn_bist320 • updated 9 days ago by Biostar ♦♦ 20
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Frequency of codon mutation in cancer
... I was curious if this metric is available at IARC or elsewhere. I would like to know how frequently a P47S (SNV) occurs across different cancer types. Or just mutation frequency at codon 47 across different cancer types. This is a validated polymorphic site but I could not obtain this piece of data ...
tcga iarc written 2.9 years ago by umn_bist320 • updated 2.8 years ago by igor7.4k
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MuTect2 - vcf 4.1 instead of vcf 4.2
... I'm using MuTect2 to call variants. The output vcf is in 4.2 format. I was wondering if there's a way to configure MuTect2 to use vcf 4.1 format instead? I've asked on the GATK forums, but wanted to reach out here to see if any of you guys knew also. Thank you very much for your help. ...
vcf gatk rna-seq mutect2 written 2.9 years ago by umn_bist320 • updated 2.8 years ago by Biostar ♦♦ 20
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[mutect2] vcf 4.1 instead of vcf 4.2?
... I'm using MuTect2 to call variants. The output vcf is in 4.2 format. I was wondering if there's a way to configure MuTect2 to use vcf 4.1 format instead? ...
vcf rna-seq mutect2 written 2.9 years ago by umn_bist320
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Comment: C: Salmon/Sailfish for repeat element quantification?
... Thank you. Just to make sure that I am understanding, according to @Devon, Salmon can map reads to the reference (in my case, consensus repeat element) without having to worry about read variants confounding my quantification results. Then I will be able to quantify repeats using Salmon, which is a ...
written 2.9 years ago by umn_bist320
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Salmon/Sailfish for repeat element quantification?
... If, instead of providing a transcriptome fasta, I use a consensus repeat element fasta (from UCSC/Repbase), would I be able to (accurately) count repeat element expression levels? Is there something conceptually/technically different between counting transcript and repeat elements? Sailfish https:/ ...
de rna-seq written 2.9 years ago by umn_bist320 • updated 2.9 years ago by thackl2.6k

Latest awards to umn_bist

Voter 3.0 years ago, voted more than 100 times.
Centurion 3.0 years ago, created 100 posts.
Rising Star 3.1 years ago, created 50 posts within first three months of joining.
Supporter 3.1 years ago, voted at least 25 times.

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