Moderator: JC

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JC6.5k
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Computational Biologist

Posts by JC

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Answer: A: Assemble genomes from different sequencing platforms
... Some assemblers allow you to combine techs as pointed before (Mira assembler for example), but answering your question, yes, it's valid to combine the contigs or scaffolds, just be aware that error rate is different between technologies and some variations could occur when you compare your sequences ...
written 11 days ago by JC6.5k
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Comment: C: randomly sample sequences of fasta file per sample name
... that bash line should work, just define "file_new" or change the name: for file in *fasta; do perl rand.pl < $file > ${file%.fasta}_subset.fasta; done ...
written 12 days ago by JC6.5k
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Answer: A: randomly sample sequences of fasta file per sample name
... Perl: #!/usr/bin/perl use strict; use warnings; my %seqs =(); $/="\n>"; while (<>) { s/>//g; my ($name, @seq) = split (/\n/, $_); my ($sp, $id) = split (/\./, $name); push @{ $seqs{$sp} }, join "\n", ">$name", @se ...
written 12 days ago by JC6.5k
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Comment: C: Fastq header modification
... Or perl: perl -pe 's/\*\*barcode\d+\/\d+\/\*\*//' < file_in > file_out ...
written 5 weeks ago by JC6.5k
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Answer: A: Can you assume variants not in VCF are all monomorphic for the reference allele?
... Definitely to be sure you need to check for coverage across all regions, if coverage is good enough and variant calling will have no problems, you can assign the position is reference homogenic. ...
written 6 weeks ago by JC6.5k
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Comment: C: Problem with adding element in a array (Perl script)
... Hi, let me comment your code and see what exactly do you want to do: #!/usr/bin/perl -w # "-w" and "use warnings" are equivalents, it's prefered to use the second use warnings; use strict; use 5.010; # You don't need back-compatibility, you can remove this ...
written 6 weeks ago by JC6.5k
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Comment: C: How to identify gene list present in Whole genome sequencing data?
... Cpapaya_113_ASGPBv0.4.annotation_info.txt file contains the annotation and mapping to Arabidopsis ...
written 6 weeks ago by JC6.5k
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Answer: A: How to identify gene list present in Whole genome sequencing data?
... If you are using a reference genome, there probably a gene annotation file (GTF, GFF3). Search in [Phytozome][1] for the annotations and try to see gene coverage, for that you can use Bamtools or similar tools. [1]: https://phytozome.jgi.doe.gov ...
written 6 weeks ago by JC6.5k
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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 11 weeks ago by JC6.5k
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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 11 weeks ago by JC6.5k

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Scholar 12 days ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 12 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
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
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