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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Computational Biologist

Posts by JC

<prev • 587 results • page 1 of 59 • next >
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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 26 days 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 4 weeks 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 5 weeks 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 7 weeks 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 8 weeks ago by JC6.8k
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Comment: C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 9 weeks 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 9 weeks ago by JC6.8k
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Answer: A: Split sequence according the 'N' base
... just for fun: #!/usr/bin/perl use strict; use warnings; $/ = "\n>"; while (<>) { s/>//g; my ($id, @seq) = split (/\n+/, $_); my @slices = split (/N+/, join("", @seq)); my $num = 0; foreach my $seq (@slices) { ...
written 9 weeks ago by JC6.8k
2
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Answer: A: How does variant callers deal with N in the reference sequence?
... In general, such positions are ignored. ...
written 9 weeks ago by JC6.8k
0
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3
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Comment: C: How To Turn A Two Column Data File Containing Pairs Into A series of clusters
... Glad to help, how large was the data? ...
written 10 weeks ago by JC6.8k

Latest awards to JC

Teacher 4 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 4 weeks ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Scholar 9 weeks 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
Appreciated 5 months ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Popular Question 5 months ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
Teacher 5 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 7 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Scholar 8 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 9 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
Teacher 9 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 10 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 11 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Scholar 18 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Solid Data From Sra
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Teacher 18 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

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