Moderator: dariober

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dariober9.3k
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Posts by dariober

<prev • 798 results • page 1 of 80 • next >
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Answer: A: Estimating the purity of tumor cells in microarray data
... Hi- If it's genotyping arrays you are referring to, then you could try [ASCAT][1]. ASCAT is designed to detect copy number variants and it gives, in addition, the purity estimate. [1]: https://www.crick.ac.uk/research/labs/peter-van-loo/software ...
written 3 days ago by dariober9.3k
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Comment: C: Why my pvalue histogram doesn't have uniform distribution
... Hi- See if this blog post helps you http://varianceexplained.org/statistics/interpreting-pvalue-histogram/ . To get better answers, it would be good to give some background about what you are testing as the U-shape may or may not be anything to worry about. ...
written 11 days ago by dariober9.3k
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Comment: C: Download of dbSNP VCF file
... To add to yours and Agata's answers (+1), indels can be extracted with `bcftools view -v indels mysnps.vcf.gz`, see [bcftools][1]. (I would resist the temptation of parsing vcf as text using per/python/awk scripts.) [1]: https://samtools.github.io/bcftools/bcftools.html ...
written 22 days ago by dariober9.3k
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Answer: A: How find correlations between ChIP-seq tracks?
... See if this script, [localEnrichmentBed.py][1], is of any help. See also https://www.biostars.org/p/195689/ [1]: https://github.com/dariober/bioinformatics-cafe/tree/master/localEnrichmentBed ...
written 25 days ago by dariober9.3k
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Answer: A: ngs vs microarray
... I don't have much experience with genotyping arrays but I think these are an example where arrays are still superior to NGS. If you want to profile a sample at known SNPs genomewide, then it's going to be difficult for NGS to beat arrays in terms of cost, amount of data to process and accuracy. I th ...
written 4 weeks ago by dariober9.3k
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Answer: A: Downstream proportions are not identical in vennpie and upsetplot results
... I haven't thought carefully about your question but the first explanation that comes to my mind is that proportional Venn diagrams with 3 or more sets are not always possible. See this post https://www.biostars.org/p/77362/. ...
written 5 weeks ago by dariober9.3k
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Comment: C: Assigning subject to query based on coverage from blast output file
... Well spotted! Corrected now. ...
written 5 weeks ago by dariober9.3k
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Comment: C: Extract PE Reads (with their mates) supporting variants in vcf file
... Just as a warning, strictly speaking, it is not possible to extract reads supporting a variant in a VCF since you don't know what reads the underlying variant caller has used. Mutect2, for example, discard reads failing some configurable options about base quality, mapping quality, flags etc plus re ...
written 8 weeks ago by dariober9.3k
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Comment: C: Extract PE Reads (with their mates) supporting variants in vcf file
... This would be a nice tool indeed. For visualization, the program I've written, [ASCIIGenome](http://asciigenome.readthedocs.io/en/latest/index.html), has the option [filterVariantReads](http://asciigenome.readthedocs.io/en/latest/commandHelp.html#filtervariantreads) that gets close to what you need ...
written 8 weeks ago by dariober9.3k
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Comment: C: Estimating cross contamination in a set of BAMS
... I was going to suggest CalculateContamination. For more detail about the method see also section VI of [mutect.pdf](https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf). ...
written 8 weeks ago by dariober9.3k

Latest awards to dariober

Popular Question 3 days ago, created a question with more than 1,000 views. For Inconsistent GTF from UCSC browser vs genePredToGtf
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Expected number of read duplicates
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 10 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 12 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Appreciated 6 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 7 months ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets

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