User: rbagnall

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rbagnall1.4k
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Posts by rbagnall

<prev • 105 results • page 1 of 11 • next >
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Comment: C: how can a DELETION be not a NULL variant?
... Precisely! In this case it is a deletion of 3 base pairs in the coding region of ROBO2 (ACAG goes to A by loss of CAG). Therefore it is an 'in-frame' deletion, which causes the protein to be shortened by one amino acid residue. ...
written 20 days ago by rbagnall1.4k
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Comment: C: Download all eQTL data for all the 9 tissues from GTEx Portal
... Yes, from here: [https://www.gtexportal.org/home/datasets][1] Scroll down to single tissue eQTL data or multi tissue eQTL data. Read the descriptions, some files are very large. [1]: https://www.gtexportal.org/home/datasets [2]: https://www.gtexportal.org/home/datasets#filesetFilesDiv15 ...
written 6 weeks ago by rbagnall1.4k
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Comment: C: How do we call this phenomenon in evolution?
... Conservative, semiconservative, and radical substitution/replacement? https://en.wikipedia.org/wiki/Conservative_replacement ...
written 7 months ago by rbagnall1.4k
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Answer: A: RNA-seq alignment rate is too low.
... I think your indexes file is incorrect. -x The basename of the index for the reference genome. You need to index the genome with hisat2-build command first. From the manual, [hisat2-build][1] builds a HISAT2 index from a set of DNA sequences. [1]: https://ccb.jhu.edu/software/hisat2/manual.sh ...
written 8 months ago by rbagnall1.4k
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Answer: A: Looking for walkthrough guide on Rare Variant Association Analysis
... Have a look at [PLINK/SEQ][1] tutorials. They give a walk through of the steps involved in exploring variation in vcf files, including different types of association tests. You should probably start at the PLINK/SEQ_101 and the extended tutorial, which have lots of informative steps on setting up t ...
written 11 months ago by rbagnall1.4k
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Answer: A: Detecting Homozygous Insertion from Sanger Seq
... Yes. 1. The Sanger sequencing trace will look very 'clean', with only single allele peaks on the chromatogram at each nucleotide (see the first 8 nucleotides of ATpoint's figure above), but there will be some additional bases compared to the reference at the site of the insertion. Some other point ...
written 11 months ago by rbagnall1.4k
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Comment: C: no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC
... Do the chromosome names in hs37d5 look like 1, 2, 3 etc, and in GRCh38 look like chr1, chr2, chr3? ...
written 12 months ago by rbagnall1.4k
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... hmm, try = "Pathogenic" rather than ~ "Pathogenic" ...
written 12 months ago by rbagnall1.4k
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... The clinvar.vcf needs to be bgzip compressed and tabix indexed first. uncompress then bgzip gunzip grch37_clinvar.vcf.gz | bgzip > grch37_clinvar.bgzip.vcf.gz tabix index tabix -p vcf grch37_clinvar.bgzip.vcf.gz view alleles in grch37_clinvar.bgzip.vcf.gz that have pathogenic in the CLNSI ...
written 12 months ago by rbagnall1.4k
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Answer: A: Find Intersections Between ClinVar Track and VCF In IGV
... You can download clinvar as a vcf, aligned to GRCh37 or GRCh38 from [here][1] The vcf INFO column contains the clinvar allele id (ALLELEID) and clinical significance, e.g. CLNSIG=Benign, CLNSIG=Pathogenic, so you could load both in IGV, or compare your vcf with the clinvar vcf for similar alleles u ...
written 12 months ago by rbagnall1.4k

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Appreciated 4 months ago, created a post with more than 5 votes. For A: Grep A Pattern From File
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Scholar 24 months ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
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