User: Justin

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Justin440
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Posts by Justin

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Vcf2Fq Not Calling Heterozygous Sites
... Oh I see, so if my REF was C and my ALT was T, it would output Y? I guess that means I should specify a reference fasta in samtools mpileup. ...
written 6.5 years ago by Justin440
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Vcf2Fq Not Calling Heterozygous Sites
... When I run the following command: samtools mpileup -g -q 50 -Q 30 -r chr1:19950062-19950062 file.bam | bcftools view -c - I get C/T as output in the 5th field: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT chr1 19950062 . N C,T 69 . DP=59;QS=0.000000, ...
written 6.5 years ago by Justin440 • updated 3.8 years ago by Biostar ♦♦ 20
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Comment: C: How Is Heterozygosity Determined In A Consensus Fasta?
... Thanks! For those interested in the math, see the heading "Consensus genotype calling" in the "Methods" section of the paper. Basically, it's a Bayesian probability model where you want P(genotype g | observed data D), which you can get from Bayes' theorem if you have P(D | g), which the paper exp ...
written 6.6 years ago by Justin440
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How Is Heterozygosity Determined In A Consensus Fasta?
... I have a consensus fasta file generated by samtools/bcftools/vcfutils as discussed in a previous post here: How to generate a consensus fasta sequence from SAM tools pileup? In some sites, I see e.g. R, which means that site was heterozygous A/G. How does it determine it's heterozygous? E.g. if yo ...
consensus samtools written 6.6 years ago by Justin440 • updated 6.6 years ago by Sean Davis26k
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Is A Genome Position In An Exon Or Intron?
... Say I have a position in the hg19 reference genome, e.g. chr1:56. How do I know programmatically if it's contained in an intron or an exon or otherwise? ...
exon intron written 6.6 years ago by Justin440 • updated 6.6 years ago by Pierre Lindenbaum127k
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Tophat Vs. Bowtie: Quality Scores
... I received 2 .bam files that were obtained from DNA-seq (they processed it with bowtie2) and RNA-seq (processed with TopHat). Let's call those DNA.bam and RNA.bam Is it normal that in the RNA.bam file, the quality scores I see are only 0, 1, 2, 3 or 50, but looking at DNA.bam, I see anything from 0 ...
tophat bowtie written 6.6 years ago by Justin440 • updated 6.6 years ago by Devon Ryan94k
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Snp Calling With Bcftools Using Pileup File Format Instead Of Bcf
... Usually when I do SNP calling, I do this: samtools mpileup -g -f Ref.fa File.bam | bcftools view -cv - where samtools outputs a bcf file and bcftools does the SNP calling. . I can also get a pileup file by running (no bcf output): samtools mpileup -f Ref.fa File.bam which is basically a list ...
calling bcftools snp written 6.7 years ago by Justin440 • updated 5.2 years ago by Biostar ♦♦ 20
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Comment: C: Tools To Calculate Conservation Of Non-Coding Rnas
... Thanks! So is it a good idea to use BLASTN for non-coding regions and for coding regions, to use TBLASTX (nucleotide vs. nucleotide, both translated in all 6 frames)? ...
written 7.4 years ago by Justin440
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Answer: A: List Of Pathway Names For Each Gene/Protein
... You can use the tool at http://www.genome.jp/kegg/tool/map_pathway1.html Under "Search against", choose "Homo sapiens" Under "Enter objects", enter the gene names in this format, example: hsa:GABRG1 hsa:GABRA2 hsa:GABRA4 hsa:GABRB1 You could probably parse the result and write a script to turn ...
written 7.4 years ago by Justin440
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Tools To Calculate Conservation Of Non-Coding Rnas
... I've read in many papers that the human non-coding RNA Xist (involved in X chromosome inactivation) is "poorly conserved" in other mammals because it only has 60% homology. Isn't 60% conservation a lot? So I thought maybe that's not a lot compared to protein coding genes that are typically very we ...
conservation written 7.4 years ago by Justin440 • updated 7.4 years ago by Chris Miller21k

Latest awards to Justin

Supporter 6.2 years ago, voted at least 25 times.
Student 6.2 years ago, asked a question with at least 3 up-votes. For Gwas Vs. Qtl Mapping?
Good Question 7.5 years ago, asked a question that was upvoted at least 5 times. For Why Do You Need To Use Cdna For Rna-Seq?
Popular Question 7.5 years ago, created a question with more than 1,000 views. For Why Do You Need To Use Cdna For Rna-Seq?
Appreciated 7.5 years ago, created a post with more than 5 votes. For Why Do You Need To Use Cdna For Rna-Seq?
Student 7.5 years ago, asked a question with at least 3 up-votes. For Why Do You Need To Use Cdna For Rna-Seq?
Student 7.6 years ago, asked a question with at least 3 up-votes. For Bidirectional Transcription
Popular Question 7.8 years ago, created a question with more than 1,000 views. For Gwas Vs. Qtl Mapping?
Appreciated 7.8 years ago, created a post with more than 5 votes. For Gwas Vs. Qtl Mapping?
Student 7.8 years ago, asked a question with at least 3 up-votes. For Gwas Vs. Qtl Mapping?
Good Question 7.8 years ago, asked a question that was upvoted at least 5 times. For Gwas Vs. Qtl Mapping?

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