Moderator: JC
JC ♦ 6.8k
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- Joined:
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Computational Biologist
Posts by JC
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... which organism?
can you use Ensembl/BioMart?
how can I bake a pie? ...
written 3 days ago by
JC ♦ 6.8k
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... you can extract samples per individual with VCFtools, then use the same strategy to count called variants ...
written 6 weeks ago by
JC ♦ 6.8k
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... You can use a bash command like:
`gunzip -c myfile.vcf.gz | grep -v "#" | cut -f1 | uniq -c`
Explanation:
- gunzip -c myfile.vcf.gz -> decompress the VCF
- grep -v "#" -> removes all header lines
- cut -f1 -> keeps only the first column (which is the chromosome id)
- uniq -c -> co ...
written 6 weeks ago by
JC ♦ 6.8k
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... There are several ways to do this, also there are unknown conditions, do you need all words including overlapped words? Do you care for words in the reverse-complement chain? The simplest solution I can think is to split your sequences and count array elements:
#!/usr/bin/perl
use stri ...
written 12 weeks ago by
JC ♦ 6.8k
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Answer:
A: Rstudio like IDE for perl
... I use Perl for many things, but I still just use regular text editors (right now I'm using [Atom][1]). The only Perl IDE I remember is [ActivePerl][2].
Or you can use [Jupyter][3] and add Perl [kernels][4]
[1]: https://atom.io/
[2]: https://www.activestate.com/activeperl
[3]: http://jupyte ...
written 3 months ago by
JC ♦ 6.8k
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... Those are field sports ;)
But what are you plotting is the contribution per dimension (that's why is an arrow or vector), for example, the values in Shot.put are correlated with an increase in Dimension 1, or 110m.hurdle is inversely correlated to the same axis. Remember that a PCA is a projection, ...
written 3 months ago by
JC ♦ 6.8k
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1
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... You can use VCFtools https://vcftools.github.io/index.html, it also contains Perl modules ...
written 3 months ago by
JC ♦ 6.8k
4
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Comment:
C: Fastq file download from pubmed
... Nothing is wrong with your file, it's a Fastq file which encodes the nucleotidic sequence and their quality, the "%" is a low-quality value in Phred+33 scale. Check https://en.wikipedia.org/wiki/FASTQ_format ...
written 4 months ago by
JC ♦ 6.8k
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2
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675
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Comment:
C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 4 months ago by
JC ♦ 6.8k
2
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2
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675
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Answer:
A: How to use igv on ubuntu
... If you are using Ubuntu 18.04 you can do `sudo apt install igv`
For previous versions you need something like:
sudo apt install default-jre
curl -LO http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.zip
unzip IGV_2.4.10.zip
cd IGV_2.4.10
sudo ln -s $PWD/igv.s ...
written 4 months ago by
JC ♦ 6.8k
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