Moderator: JC

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JC6.6k
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Computational Biologist

Posts by JC

<prev • 582 results • page 1 of 59 • next >
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Comment: C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 5 days ago by JC6.6k
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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 6 days ago by JC6.6k
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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 6 days ago by JC6.6k
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Answer: A: How does variant callers deal with N in the reference sequence?
... In general, such positions are ignored. ...
written 6 days ago by JC6.6k
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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 13 days ago by JC6.6k
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Answer: A: How To Turn A Two Column Data File Containing Pairs Into A series of clusters
... You can use perl or python to get that: #!/usr/bin/perl use strict; use warnings; my %g = (); my $a = undef; my $b = undef; my $net = 0; my $fst = 1; while (<>) { chomp; ($a, $b) = split (/\s+/, $_); if ($fst == 1) { ...
written 16 days ago by JC6.6k
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Answer: A: What is the exact number of gene that we can detect from differentially expresse
... Cancer is highly variable, even tumours from the same patient are different, you can see this in a PCA or similar plot. So it's not surprising that you get 6k DEG, beside FC, you can also filter by the number of samples sharing the gene as DEG, like filtering by genes as DE in 50% of your samples. ...
written 16 days ago by JC6.6k
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Answer: A: Bioconductor - DESeq
... Answering your 3 questions: 1. Yes, you can compare Acinar (A), Duct (D) and controls (C) but I would contrast (A / C) vs (D / C) and then get DEG between groups, that will mean to get genes differentially expressed to the control and differential expressed between A / D. But if you only care about ...
written 18 days ago by JC6.6k
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Comment: C: Bioconductor - DESeq
... Hi Soheila, I just formatted your post and tagged as Question, because this is not a "Tutorial". ...
written 18 days ago by JC6.6k
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Answer: A: How to convert vcf format with 0/0 0/1 1/1 to SNP
... I'm assuming that you want to convert each VCF record into the genetic variant observed, so "0/0" is considered "C" and "1/1" is "A" and "0/1" is "CA". #!/usr/bin/perl use strict; use warnings; while (<>) { if (/^#/) { print; next; } ...
written 4 weeks ago by JC6.6k

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Scholar 6 days ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 6 days 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 6 days 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
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Popular Question 3 months ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
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
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