User: dariober

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dariober8.2k
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Posts by dariober

<prev • 703 results • page 1 of 71 • next >
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Comment: C: Making UpSetR plot with title
... Yes... ImageMagick is quite a universe in itself, I just know the bare surface of it! ...
written 2 days ago by dariober8.2k
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Comment: C: Making UpSetR plot with title
... Hi- Glad you found a solution, but see my edit to set font. ...
written 2 days ago by dariober8.2k
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Answer: A: Making UpSetR plot with title
... Half-baked solution is to add the title to the image itself using the [convert][1] tool part of the ImageMagick suite. At least you can do it programmatically. For example: convert -gravity North -annotate +0+0 'My Title' -pointsize 20 input.png output.png This will add the text "My Title" on ...
written 2 days ago by dariober8.2k
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Answer: A: How to extract reads with a known variant form a bam file
... One more answer... If you are interested in visually inspecting these reads, the program I've written, [ASCIIGenome][1], has a command, [filterVariantReads][2], to filter for reads that are variant at a given position or interval. So, first load genome and data: ASCIIGenome -fa genome.fa aln. ...
written 7 days ago by dariober8.2k
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Comment: C: WTSI Mutational Signature Framework: matlabpool function
... A little late but since I'm facing the same situation... Some good soul seems to have ported the WTSI Mutational Signature Framework to R, see [mutSignatures][1] and [SomaticSignatures][2]. (P.S. I would vote to re-open this question) [1]: https://cran.r-project.org/web/packages/mutSignatures/i ...
written 13 days ago by dariober8.2k
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Answer: A: Why the optimal value of BQSR intervals is 20
... Since this question has returned to the top, I'll give it a shot answering... Base quality recalibration as implemented in the GATK interface consists of two steps. The first step collects statistics about biases, the second step actually edits the bam records to recalibrate them. The first step ...
written 19 days ago by dariober8.2k
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Answer: A: perplexity value in t-sne algorithm
... In practice, I think you should just try a few values and see which one(s) "makes sense". It's a hand-waving suggestion of course but after all, t-SNE is a visualization method so there isn't really a correct or optimal way of doing it, there is no statistical hypothesis or test involved. It depends ...
written 23 days ago by dariober8.2k
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Answer: A: BWA mem and BWA aln lead to different results
... > this leads to two diffrent genetic structures for the same population! Provided that there are no bugs in your analysis pipeline, I think the question is not so much which aligner is better but rather on whether there is an actual population structure or whether the two different structures ar ...
written 23 days ago by dariober8.2k
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Comment: C: BQSR: when it is applicable?
... Hi- It would be good if Heng Li would chime in here... I think Heng makes that statement with reference to just the two datasets used in the paper. I don't think he meant to generalize more broadly. On the other hand, in this recent paper, [ Callari et al. Intersect-then-combine approach...][1], the ...
written 25 days ago by dariober8.2k
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Comment: C: BQSR: when it is applicable?
... Hi John- Thanks for the input and for putting in some numbers. > 10 million SNPs in dbSNP (there's 13million now). Wait, dbSNP currently has [324 million SNPs][1] which makes a few million SNPs per individual reasonable. > That puts the SNP rate per person at i guess 1 in 30000bp, which is ...
written 26 days ago by dariober8.2k

Latest awards to dariober

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 2 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 7 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 25 days ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Great Question 10 weeks ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Student 3 months ago, asked a question with at least 3 up-votes. For ChIP-Seq: Calling peaks with replicates
Appreciated 3 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 4 months 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
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Great Question 5 months ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 7 months ago, created a question with more than 1,000 views. For Java Samtools Api: Write Bam To Stdout
Teacher 7 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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