Moderator: Ketil

gravatar for Ketil
Ketil3.8k
Reputation:
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Location:
Germany
Website:
http://blog.malde.org/
Last seen:
1 week, 6 days ago
Joined:
6 years, 9 months ago
Email:
k****@malde.org

Posts by Ketil

<prev • 276 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 6 weeks ago by Ketil3.8k
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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 bcf samtools bcftools written 6 weeks ago by Ketil3.8k • updated 5 weeks ago by d-cameron1000
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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 10 months ago by Ketil3.8k
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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 10 months ago by Ketil3.8k
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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 10 months ago by Ketil3.8k
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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 10 months ago by Ketil3.8k
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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 3.5 years ago by Ketil3.8k
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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 4.1 years ago by Ketil3.8k
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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 4.1 years ago by Ketil3.8k
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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 4.1 years ago by Ketil3.8k

Latest awards to Ketil

Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How To Convert (Aligned) Text File Into An Alignment File?
Librarian 9 months ago, created a post with more than 10 bookmarks. For Selecting Random Pairs From Fastq?
Great Question 9 months ago, created a question with more than 5,000 views. For Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Microarrays And Gene Regulation
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