Moderator: JC

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JC7.6k
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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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Answer: A: Transcript quantification using the reference transcriptome(gencode) and the raw
... if the gene models are correct and you want only to quantify known genes, it is perfectly fine. ...
written 3 days ago by JC7.6k
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Answer: A: Question about combining (technical?) replicates
... if there are no big bias yes, after processing just check libraries in a PCA, if there are no big differences you can merge them ...
written 3 days ago by JC7.6k
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Comment: C: basic experimental methods book for bioinformaticians
... A simple book could be hard to create, each methodology is based on a lot of biological knowledge. Even biologists don't understand the methods they do, many experiments are based on "faith". Coming from a wet lab I know many people cannot explain the methods, like "don't do a PCR on a moon night be ...
written 4 days ago by JC7.6k
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Comment: C: transcripts assemble by StringTie
... are you using: ftp://ftp.ensemblgenomes.org/pub/release-42/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz ftp://ftp.ensemblgenomes.org/pub/release-42/plants/gtf/triticum_aestivum/Triticum_aestivum.IWGSC.42.gtf.gz ? ...
written 6 days ago by JC7.6k
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Comment: C: How to create a tab delimited file?
... true, I modify the code to read the file name from another var ...
written 10 days ago by JC7.6k
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Comment: C: How to create a tab delimited file?
... The `while (<$infile>) {}` loop reads the file line per line ...
written 10 days ago by JC7.6k
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Answer: A: fastq reads cleaning
... Any good bioinformatician will run a QC before doing anything and perform cleaning if needed. I think it is omitted because of that and recent Illumina protocols returns cleaned reads. I don't remember last time I cleaned some Illumina data since the HiSeq 2000. ...
written 11 days ago by JC7.6k
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Comment: C: transcripts assemble by StringTie
... Sadly, even when the genome and version are named equally in NCBI and Ensembl, the sequences names could be different. Use genome and annotation from the same source to ensure you have the same naming. ...
written 11 days ago by JC7.6k
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Answer: A: How to create a tab delimited file?
... There are some Perl-ings you need to understand first: my $infile = $ARGV[0]; This line reads the first command line argument after your script name and pass to the variable **$infile** open (my $infile, "<", "namconvmars.txt") or die "Can't read from $infile: $!"; You are declar ...
written 11 days ago by JC7.6k
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Answer: A: How to add header name to all annotation lines
... Perl: #!/usr/bin/perl use strict; use warnings; my $head = ''; while (<>) { chomp; if (/^(@.+)/) { $head = $1; } else { print "$_\t$head\n"; } } Run as `perl addheader.pl < INPUT > OUPUT` ...
written 11 days ago by JC7.6k

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Teacher 18 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 4 weeks ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
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Teacher 8 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
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 3 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
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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
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Scholar 8 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
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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
Scholar 9 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
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