User: rbagnall
rbagnall • 1.4k
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Posts by rbagnall
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2
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... 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
rbagnall • 1.4k
0
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4
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5.4k
views
4
answers
... 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
rbagnall • 1.4k
0
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0
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... Conservative, semiconservative, and radical substitution/replacement?
https://en.wikipedia.org/wiki/Conservative_replacement ...
written 7 months ago by
rbagnall • 1.4k
0
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2
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565
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2
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... 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
rbagnall • 1.4k
0
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2
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1.0k
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2
answers
... 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
rbagnall • 1.4k
3
votes
3
answers
744
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... 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
rbagnall • 1.4k
0
votes
0
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753
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... 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
rbagnall • 1.4k
1
vote
1
answer
538
views
1
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... hmm, try
= "Pathogenic"
rather than
~ "Pathogenic" ...
written 12 months ago by
rbagnall • 1.4k
1
vote
1
answer
538
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1
answers
... 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
rbagnall • 1.4k
3
votes
1
answer
538
views
1
answers
... 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
rbagnall • 1.4k
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