Moderator: JC

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JC6.8k
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Mexico
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http://about.me/jcabal...
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Joined:
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Computational Biologist

Posts by JC

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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... which organism? can you use Ensembl/BioMart? how can I bake a pie? ...
written 3 days ago by JC6.8k
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Comment: C: how to count variants by chromosome in a vcf file?
... you can extract samples per individual with VCFtools, then use the same strategy to count called variants ...
written 6 weeks ago by JC6.8k
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Answer: A: how to count variants by chromosome in a vcf file?
... 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 JC6.8k
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Answer: A: count word ocurrences in fasta file
... 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 JC6.8k
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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 JC6.8k
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Comment: C: How to interpret PCA output statistically and biologically
... 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 JC6.8k
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Answer: A: merging of multi samples tabix and bzipped vcf files into one vcf file using Per
... You can use VCFtools https://vcftools.github.io/index.html, it also contains Perl modules ...
written 3 months ago by JC6.8k
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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 JC6.8k
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Comment: C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 4 months ago by JC6.8k
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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 JC6.8k

Latest awards to JC

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 3 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Scholar 4 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Scholar 4 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 4 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Scholar 6 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Appreciated 7 months ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 9 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Scholar 10 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 11 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Scholar 20 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Solid Data From Sra
Scholar 20 months ago, created an answer that has been accepted. For A: How to check whether the mate read is fully mapped or not?

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