Moderator: JC

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JC6.4k
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Computational Biologist

Posts by JC

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Comment: C: How to fetch those line having only similar characters.
... hi, not sure what do you want to print, just a "\n" if the line contains a homozygous base? or just for A,A, T,T? what you need is to extend the last if, something like: `perl -lne '%a = (); @b = split /,/, $_; foreach $b (@b) { $a{$b}++; }; @b = keys %a; if ($#b > 0) { print } else { print "\n ...
written 19 days ago by JC6.4k
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Comment: C: How to fetch those line having only similar characters.
... Another Perl solution: `perl -lne '%a = (); @b = split /,/, $_; foreach $b (@b) { $a{$b}++; }; @b = keys %a; print if ($#b > 0)' < in.txt` A,T,A, G,T, A,T,A, T,C, G,G,G,A, A,T,G,C ...
written 20 days ago by JC6.4k
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Answer: A: The exon of a variant
... The gene has 3 transcripts (NM_001135585, NM_003039 and NM_001328619), in the first and second transcripts, your variant is in exon3, meaning that probably the transcripts have the same first three exons but are different at some point after that. The third transcript is different, and the variant e ...
written 4 weeks ago by JC6.4k
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Answer: A: Merging of sequence chunks
... Perl option: #!/usr/bin/perl use strict; use warnings; my %seqs = (); # load sequences $/ = "\n>"; # ingest all fasta sequences while (<>) { s/>//g; my ($name, @seq) = split (/\n/, $_); #$name =~ s/@.+//; # uncomment ...
written 10 weeks ago by JC6.4k
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Answer: A: Curiosity about Klinefelter syndrome
... Not directly for this, but a good QC in any genomic pipeline is to check chromosome coverages or regions with high-mutation rates reporting when something is far from the standards. ...
written 11 weeks ago by JC6.4k
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Answer: A: What made you interested in Bioinformatics?
... I was hooked by the possibility to understand the biology behind the data and to use HPC for this. ...
written 11 weeks ago by JC6.4k
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Comment: C: Fail running blastdb and blastn on my own computer
... use something like "program\ files" ...
written 3 months ago by JC6.4k
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Comment: C: error while using cutadapt
... you need to install it ;) sudo apt-get install dos2unix ...
written 3 months ago by JC6.4k
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Comment: C: Fail running blastdb and blastn on my own computer
... I recommend to use the WSL in Win10, it works wonderfully. ...
written 3 months ago by JC6.4k
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Answer: A: The most exciting and regret moment for a bioinformatician
... I believe that is a common job interview question, in general, it is used to check with the candidate what are his/her expectations and what consider important in his/her career. It also depends on the background, a biologist entering into bioinformatics will be excited about CS stuff and vice-versa ...
written 3 months ago by JC6.4k

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