User: Vivek

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Vivek1.5k
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Bioinformatics Developer

Posts by Vivek

<prev • 203 results • page 1 of 21 • next >
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Comment: C: how to analyse gene expression using RNA-seq data
... In guided transcriptome assembly you give the assembler a GTF file of known transcripts/isoforms for the organism you are interested in to aid as a guiding reference. In unguided assembly, you don't which can lead the assembler into assembling more de novo isoforms, if that is your objective. ...
written 3 days ago by Vivek1.5k
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Answer: A: how to analyse gene expression using RNA-seq data
... You could visit a few RNA seq tutorials. They are by far the easiest to find in bioinformatics. Alternatively you can read through the manuals for the cufflinks suite. http://cole-trapnell-lab.github.io/cufflinks/manual/ The basic workflow is Reads -> Mapping to genome (STAR/Tophat etc are good ...
written 3 days ago by Vivek1.5k
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Answer: A: SVM based Filtering For NGS data
... As far as I'm aware, the only ML based software tool for variant filtering is the GATK's variant quality score recalibration and it uses a Gaussian mixture model. http://gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr ...
written 21 days ago by Vivek1.5k
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Comment: C: Mapping two WGS Data
... You still need a reference genome to align using Magic Blast, which you do not have if you are comparing two sets of sequencing reads against each other. If I were you, I'd assemble the reads using SOAPdenovo and then align the resulting assemblies using BLAT. ...
written 25 days ago by Vivek1.5k
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Answer: A: Mapping two WGS Data
... You need to give more information. What is the read length? Are there multiple insert size libraries? Your choice of assembler would depend on that. Ideally you'd assemble them separately and align them using something like BLAT. ...
written 25 days ago by Vivek1.5k
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Answer: A: Annovar Output column "AAChange.knowngene" gives different values
... Annovar is giving you the annotation with reference to each transcript within the gene, which is the right way for an annotation program to give results. The practical way to prioritize these is to rank the amino acid change in order of severity, possibly with functional annotation scores and predic ...
written 26 days ago by Vivek1.5k
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Comment: C: SNP website Development Site
... What data do you plan to work with? If you want to upload variants and get annotations, there is Variant Effect Predictor, which is quite effective. If you want people to upload their BAM files or fastq reads to a website and get variant calls, you are likely looking at the wrong solution as no one ...
written 26 days ago by Vivek1.5k
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Comment: C: missing the variant NM_000251.2(MSH2):c.942+3A>T in variant calling
... It looks like a single base heterozygous deletion from the first screenshot rather than an A>T change. ...
written 4 weeks ago by Vivek1.5k
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Comment: C: identifying mutation & copy numbers using sequencing data
... I was mentioning more in the sense of genotyping known cnvs where you have phenotypes being identified with a deletion in one chromosome plus a damaging SNP on the other. If novel cnvs are your target then yeah wgs is your best and probably only option. ...
written 8 weeks ago by Vivek1.5k
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Answer: A: identifying mutation & copy numbers using sequencing data
... If you have the budget for whole genome sequencing, that would be top choice. Otherwise exomes would be fine as long as your CNVs of interest are expected to be included in targeted capture regions. ...
written 8 weeks ago by Vivek1.5k

Latest awards to Vivek

Scholar 25 days ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 9 weeks ago, created an answer that has been accepted. For A: Identify overlapping coordinates
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Appreciated 7 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 8 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
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