Moderator: Ketil

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Ketil4.0k
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http://blog.malde.org/
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Posts by Ketil

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Comment: C: Estimating genome size
... I found some wild sequences, and ran the k-mer analysis. This gives slightly over 1Gbp. Will do mapping coverage when I get the BAM files. ...
written 7 weeks ago by Ketil4.0k
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Comment: C: Estimating genome size
... As mentioned, I used jellyfish to do this. With kmers of 21, 25, 29, and 31, I get k-mer coverages of 20, 19, 18 and 17, and genome size esimates of 975, 981, 986 and 1017 Mbp respectively. ...
written 7 weeks ago by Ketil4.0k
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Comment: C: Estimating genome size
... As far as I can tell, it is a regular diploid animal (copepod). One hypothesis is that the inbred specimens used for sequencing have lost parts of the genome, while the genome size experiments were done on wild specimens. I have sequences from wild individuals too, but currently they are unavailab ...
written 7 weeks ago by Ketil4.0k
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Estimating genome size
... So I am trying to estimate the size of a genome, and getting confusing and inconsistent results. So far I have: - assembly size. All of them tend towards a cumulative size 600-700 Mbp assemblies, depending on the assembler and what sequence data is used, with the higher numbers from assemblies c ...
genome assembly sequencing written 7 weeks ago by Ketil4.0k • updated 7 weeks ago by JC11k
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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 3.0 years 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 3.0 years ago by Ketil4.0k • updated 16 months ago by ATpoint40k
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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 3.7 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 3.7 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 3.7 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 3.7 years ago by Ketil4.0k

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