Moderator: dariober

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dariober9.9k
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Posts by dariober

<prev • 836 results • page 1 of 84 • next >
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Answer: A: Error using Tabix
... The vcf file you got from ftp://ftp.sra.ebi.ac.uk/vol1/ERZ696/ERZ696780/chr8_eva.vcf.gz seems defective since its header does not contain the contig "8". As a quick and dirty fix you can add the missing contig with something like: gunzip -c chr8_eva.vcf.gz | grep '^##' > chr8_eva.fix.vcf ...
written 12 days ago by dariober9.9k
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Answer: A: Can BWA restart a calculation after a break?
... A dumb solution may be to split the input fastq files in chunks small enough to fit the 24h limit, align each file-chunk and then merge. For file splitting, unix comes with the handy split command that you can use e.g. as: zcat reads.R1.fq.gz | split -l 40000000 - reads.R1.fq.split zcat rea ...
written 22 days ago by dariober9.9k
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Comment: C: How to generate a short sequence that does not align to the RefSeq?
... Keep in mind also that to ask for a sequence that does not align you need to decide what makes an alignment valid (e.g, maximum number of mismatches or minimum percent identity, E-value, etc). If you don't define any constraint, then any sequence can be aligned to any other sequence by allowing enou ...
written 26 days ago by dariober9.9k
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Comment: C: Changing file name with sed command
... +1 Pierre > every time you put a '#' or a '=' in a filename, god kills a kitten. Then we have the culprit for wars and famines: spaces in filenames. ...
written 4 weeks ago by dariober9.9k
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Comment: C: How does bcftools isec do the intersection?
... Hi- To add to your answer, maybe worth mentioning that with the option [--collapse][1] you can control what makes intersecting records compatible [1]: https://samtools.github.io/bcftools/bcftools.html#common_options ...
written 4 weeks ago by dariober9.9k
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Comment: C: How can I convert -log10 (p-value) to p-value?
... In my own words (don't take them too seriously), the log can be interpreted as *how many times* a value is greater or smaller than the baseline of 1. So for example, a log10 of 2 means *100 times more than the baseline* while a log10 of -2 means *100 times smaller than the baseline*. In fact, log(1) ...
written 4 weeks ago by dariober9.9k
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Answer: A: How can I convert -log10 (p-value) to p-value?
... Hi- The opposite of logarithm is exponentiation. So take the base of the logarithm (10 in your case) and exponentiate it to the result of the log. E.g. in R: p<- 0.01 logp<- -log10(p) # = 2 # Undo log: 10^-logp # = 0.01 # And: 10^-11.28 # = 5.248075e-12 ...
written 4 weeks ago by dariober9.9k
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Answer: A: Return number of mismatches for multiple sequences
... A while back I had a similar problem and I ended up writing [SequenceMatcher](https://github.com/dariober/SequenceMatcher/), a wrapper around the alignment tools in [BioJava][1]: Basically: java -jar SequenceMatcher.jar match -a reference.fa -b queries.fa The output gives you the number of mi ...
written 5 weeks ago by dariober9.9k
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Comment: C: Convert indel list with [-/A] notation to VCF with adjacent base
... > Indels are more tricky, since proper VCF needs the adjacent base I think [bcftools norm](https://samtools.github.io/bcftools/bcftools.html#norm) should do the trick with something like (not tested at all): awk 'code to shuffle columns into vcf' $infile \ | bcftools norm -c s -f ref.fa ...
written 6 weeks ago by dariober9.9k
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Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
... I'd like to bring to your attention [cnv_facets](https://github.com/wwcrc/cnv_facets), a command line tool for detecting copy number variant (CNV), based on the [facets][1] package (*Shen R and Seshan VE, Nucleic Acid Res, [2016][2]*). Recently I've been using the facets package for detecting CNVs ...
tool cancer somatic command line facets cnv written 9 weeks ago by dariober9.9k

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Student 20 hours ago, asked a question with at least 3 up-votes. For Are ENA and SRA archives in sync?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
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Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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