User: Clare

gravatar for Clare
Clare150
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150
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United States
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2 years, 9 months ago
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7 years, 5 months ago
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Posts by Clare

<prev • 12 results • page 1 of 2 • next >
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How to get GQX annotation in vcf file
... I need to analyze both variant and nonvariant sites from a vcf. I produced this with GaTK Haplotype caller (v 3.7), but I'm struggling to know how to filter the variant and nonvariant sites 'fairly'. Illumina states you can do this using the GQX value, but my GATK gvcfs and vcfs don't have that anno ...
snp filtering written 2.8 years ago by Clare150 • updated 2.2 years ago by Kevin Blighe66k
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Comment: C: equivalent of bash eval in R
... Wow - thank you!! Thats perfect ...
written 6.5 years ago by Clare150
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equivalent of bash eval in R
... I have a newbie R question.  So my data are Loci names and allele frequencies. The loci and associated allele frequences I have as a list of vectors called dat. I also have another list 'locusnames' with just the locus names.  See below - but note this is a subset I'm working with of just a few loci ...
R loop written 6.5 years ago by Clare150
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Comment: C: Fastq-Dump Quality Scores Off Scale
... Also - The command works on data from a different project - i.e. gives me Q33. So it must be a data issue with this specific data project. ...
written 6.6 years ago by Clare150
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Fastq-Dump Quality Scores Off Scale
... I used SRA toolkit (sratoolkit.2.3.4-2-mac64) to convert some paired end read data from .sra to .fastq using: fastq-dump -I --split-files SRR1062090.sra The default option is Q33 quality scores - but checking the outfile I see the quality scores were clearly illumina 1.5. @SRR1062090.1.1 BRISCOE:7 ...
sra written 6.6 years ago by Clare150 • updated 6.6 years ago by Devon Ryan97k
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Sam To Bam - Loss Of Data Or Just Great Compression?
... I use picard tools to take a BWA alignment sam file and convert it into a sorted bam file. Normally this works well, but for a small number of samples, I am getting VERY small bam files. e.g. SAM file = 42G, BAM file = 831M Samtools produces the same BAM file size. If I take the bam and convert it ...
picard sam bam written 6.7 years ago by Clare150 • updated 6.7 years ago by Chris Miller21k
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Cigar String - Are Soft Clipped Reads Only Ever At The Start Or End?
... Forgive this basic question, but with a cigar string, are soft clipped reads only ever seen at the start or end of the read and cigar string? i.e. 2S80M or 80M1D5S NOT 20M5S30M ...
cigar written 6.9 years ago by Clare150 • updated 6.9 years ago by Ashutosh Pandey12k
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Comment: C: How Does Ld In Plink Work?
... Sorry for my absence - I haven't been checking my email. I wonder if its the --ld-window 20 command. With this you are saying that you only want to analyse SNPS that are not more 20 SNPs apart. I'm not sure why you would want to do that for your task you are trying to do. Try removing that option ...
written 6.9 years ago by Clare150
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Comment: C: How Does Ld In Plink Work?
... slightly updated from first post..... ...
written 7.0 years ago by Clare150
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Answer: A: How Does Ld In Plink Work?
... So there are various plink options --ld-window-kb 1000 # This means only assess LD between SNPs within a specified window i.e. here within 1000 kb. With whole genome data, there are so many SNPs, you don't want to compare every snp to every other snp - the outfile would be too big. So this specifi ...
written 7.0 years ago by Clare150

Latest awards to Clare

Appreciated 6.4 years ago, created a post with more than 5 votes. For A: How Does Ld In Plink Work?
Good Answer 6.4 years ago, created an answer that was upvoted at least 5 times. For A: How Does Ld In Plink Work?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Cigar String - Are Soft Clipped Reads Only Ever At The Start Or End?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Fastq-Dump Quality Scores Off Scale
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Remove Soft Clipped Bases
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Sam To Bam - Loss Of Data Or Just Great Compression?
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: How Does Ld In Plink Work?

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