Moderator: Ketil

gravatar for Ketil
Ketil4.0k
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Location:
Germany
Website:
http://blog.malde.org/
Last seen:
1 year, 10 months ago
Joined:
8 years, 8 months ago
Email:
k****@malde.org

Posts by Ketil

<prev • 275 results • page 1 of 28 • next >
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Comment: C: What does <*> mean in a vcf file?
... I didn't use --variants-only (it's not an option to 'bcftools consensus', which I used). The output is from samtools and not bcftools, anyway. Thanks for the code pointer, but I can't really understand how this is supposed to work. ...
written 24 months ago by Ketil4.0k
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What does <*> mean in a vcf file?
... Hi, I'm running samtools (version 1.3.1, Ubuntu 17.04 default) to generate a VCF from a reference and some BAM files: samtools mpileup --ff 0x800 -r my_contig -v -f my_genome.fa *.bam -o my.vcf But in the VCF file, all lines have a format like: my_contig 4 . A <*& ...
vcf bcftools samtools bcf written 24 months ago by Ketil4.0k • updated 4 months ago by ATpoint24k
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Answer: A: The number of cluster in Kmean clustering
... There's an interesting modification to k-means where instead of setting the clusters explicitly, you minimize the expression $\sum || x_i - \mu_i ||^2 + \sum || \mu_i - \mu_j ||$ (IIRC). The $\mu$s represent cluster centroids, and the minimization forces them to be as few as possible, while ...
written 2.7 years ago by Ketil4.0k
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Answer: A: How to print the lines exclusively from unknown columns with missing(undef) valu
... > I wanna print just the columns in which IDs present missing ("null" or "undefined") values, i.e. they're blank. If this is actually what you want, you could identify columns with blanks, something like: `for i in {1..10}; do cut -f$i < file | grep -q '^$' || echo $i; done` and then to pr ...
written 2.7 years ago by Ketil4.0k
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Comment: C: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
... Still here? :-) Yes, I maintain the current hash in forward and reverse complement, shift left/right and chop off the end, add next base, and store the numerically smallest hash. Code at [https://github.com/ketil-malde/kmx][1]. [1]: https://github.com/ketil-malde/kmx ...
written 2.7 years ago by Ketil4.0k
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Comment: C: "No space left on device" after "Finished constructing BWT"
... I wouldn't trust them, bwa is perhaps more robust than your typical bioinformatics program, but chances are one or more of the files are incomplete, and that further processing will give you incomplete or wrong results - or if you are lucky, you will get an error. ...
written 2.7 years ago by Ketil4.0k
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Comment: C: sam errors generated from bwa mem
... Seems like a bug in bwa?  I've had a ton of trouble after having an error in the reference file (two contigs were concatenated), this wasn't properly picked up by any of the tools I used, and produced corrupt/incorrect output.  I can only suggest that you double-check all input files, and if nothing ...
written 5.4 years ago by Ketil4.0k
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Comment: C: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
... I did an implementation of this in Haskell - normally, I'd expect a high level language to be less efficient for this, but it turns out it is fast enough (meaning that I haven't found an associative data structure that won't be dramatically slower than the hashing). I can hash about 40MB/s on my la ...
written 5.9 years ago by Ketil4.0k
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Comment: C: A Question About Hybrid Assembly
... Euler is just an early de Bruijn assembler, in principle, it is the same as ALLPATHS, Velvet, and Abyss. ...
written 5.9 years ago by Ketil4.0k
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Comment: C: What Does Samtools Flagstat Results Mean?
... I'm pretty sure 'total' is the total number of alignments (lines in the sam file), not total reads. ...
written 6.0 years ago by Ketil4.0k

Latest awards to Ketil

Great Question 2.7 years ago, created a question with more than 5,000 views. For Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
Librarian 2.7 years ago, created a post with more than 10 bookmarks. For Selecting Random Pairs From Fastq?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: How To Convert (Aligned) Text File Into An Alignment File?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Microarrays And Gene Regulation
Prophet 5.3 years ago, created a post with more than 20 followers. For Selecting Random Pairs From Fastq?
Epic Question 5.3 years ago, created a question with more than 10,000 views. For Selecting Random Pairs From Fastq?
Great Question 5.3 years ago, created a question with more than 5,000 views. For Selecting Random Pairs From Fastq?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Lua For Bioinformatics?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Selecting Random Pairs From Fastq?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Estimating Probability Of Differing Allele Frequencies From Pooled Samples
Commentator 5.3 years ago, created a comment with at least 3 up-votes. For C: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Oligo Design From Ests
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Adapter/Linker/Primer Sequence Database?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For What Assembler To Use For Eukaryotes?
Commentator 5.3 years ago, created a comment with at least 3 up-votes. For C: How To Convert (Aligned) Text File Into An Alignment File?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Alternative To "Samtools.Pl Pileup2Fq" For Consensus Generation?
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: [Discussion] Parsing Fasta Without Bioperl
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: What Additional Computer Science Courses Should I Do As A Bioinformatician
Appreciated 5.3 years ago, created a post with more than 5 votes. For A: What'S The Best Generic Scripting Tool For Bioinformatics?
Appreciated 5.7 years ago, created a post with more than 5 votes. For What Assembler To Use For Eukaryotes?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Soapdenovo Assembly Quality Assessment
Appreciated 5.7 years ago, created a post with more than 5 votes. For Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: How Does Assembled Contigs Get Mapped To A Chromosome?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: About Paired-End Sequencing

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