User: bioinfo89
bioinfo89 • 40
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Posts by bioinfo89
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Comment:
C: bedtools complement error
... Hi @Alex Reynolds,
I was just exploring the bedpos `--complement` option instead of bedtools complement option to get coordinates which are present in `genome.bed` but not in `target.bed`, I found `--difference` is more suitable to get the `result.bed`, instead of `--complement`.
Do correct me if ...
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... Hi @ATpoint,
Thank you very much for the Rscript, I used it for extracting the homopolymers from reference genome. I wanted to know if there is a way to use the same script to limit the homopolymers finding in the coding regions only?
...
written 11 weeks ago by
bioinfo89 • 40
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... Hi @ATpoint,
I would really appreciate if you could share the Rscript again. I couldn't find your Rscript.
Thanks! ...
written 11 weeks ago by
bioinfo89 • 40
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... Hello All,
My query is regarding the genomic positions to be considered for a variant which are present in the intron.
For example: c.5278-1G>C, so the genomic position for c.5278 is 41203134.
Since the above nomenclature is 5278-1 which will be 5277th position and is the last base of the intr ...
written 4 months ago by
bioinfo89 • 40
• updated
4 months ago by
finswimmer ♦ 12k
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... Yes, I am trying my best. :) ...
written 8 months ago by
bioinfo89 • 40
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... By non-standard vcf I mean, it is a dbSNP submission VCF format which has additional information about the study and methods etc along with the reference assembly ID, INFO and FORMAT fields. Also, the INFO and FORMAT fields I had to remove since the tabidx step was not able to parse the information. ...
written 8 months ago by
bioinfo89 • 40
• updated
8 months ago by
WouterDeCoster ♦ 40k
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... Yes sure I will test the vcflib tool kit thanks for the info.
I used the following commands for vcftools:
/home/tools/tabix-0.2.6/bgzip Validated.vcf
/home/tools/tabix-0.2.6/tabix -p vcf Validated.vcf.gz
/home/tools/vcftools_0.1.13/perl/vcf-compare Validated1.vcf.gz Validated2.vcf ...
written 8 months ago by
bioinfo89 • 40
• updated
8 months ago by
WouterDeCoster ♦ 40k
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... I tried it. But since the file I am using is not a standard VCF file, I am not getting the desired output. The vcf-validator throws lots of errors when I check the files I am using. ...
written 8 months ago by
bioinfo89 • 40
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5 follow
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... Hi All,
I am working on 1000g data. So I have 25 tab-delimited text files corresponding to each population. Each file has jointly genotyped data, so it contains genotypes from all the samples (~60-120) per population in the VCF.
Format of the File:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMA ...
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... Yes that's true but the hg19 reference (UCSC version) uses NC_001807 version for chrM mentioned here : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/.
It has not been updated to the NC_012920.1 for hg19. This is the reason why I want to convert my variants to the latest version but I am no ...
written 9 months ago by
bioinfo89 • 40
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For Merge vcf files with multiple samples into one vcf with all variants
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For A: How to extract unique paired end reads from a merged BAM file?
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