Moderator: JC

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JC9.1k
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Mexico
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http://about.me/jcabal...
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7 years, 6 months ago
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Computational Biologist

Posts by JC

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Comment: C: Where can I find list of housekeeping(HK) genes?
... Many normalization methods don't preselect genes, for example, TMM algorithm in EdgeR looks for the more stable genes in your data. ...
written 3 days ago by JC9.1k
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Comment: C: Remove character from Fasta IDs -- python
... Check how to write to file in python https://www.guru99.com/reading-and-writing-files-in-python.html ...
written 5 days ago by JC9.1k
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Comment: C: Hg38 to b37 LiftOver chain?
... The UCSC doesn't provide liftOver to b37, you can use hg19 instead unless you expect differences in your analysis, here is an explanation of the different version: https://software.broadinstitute.org/gatk/documentation/article?id=23390 ...
written 5 days ago by JC9.1k
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Comment: C: Calculating Shannon entropy for RNA sequences in multi-fasta using rnaentropy
... glad to help, good luck with your research ...
written 5 days ago by JC9.1k
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Comment: C: Difference in R1 and R2 FASTQ files from RNA seq paired end
... yes, it could be a cause of the filtering ...
written 5 days ago by JC9.1k
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Answer: A: Calculating Shannon entropy for RNA sequences in multi-fasta using rnaentropy
... I wouuld use a Perl (or Python script) to parse the multifasta and run your tool, like: #!/usr/bin/perl use strict; use warnings; $/="\n>"; # read fasta sequences in blocks while (<>) { s/>//g; my ($id, @seq) = split (/\n/, $_); m ...
written 6 days ago by JC9.1k
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Answer: A: Converting amino acid sequences to numerical values
... here how I could do in Perl: #!/usr/bin/perl use strict; use warnings; $ARGV[2] or die "use convert.pl ref_data fasta_in fasta_out\n"; my $ref_file = shift @ARGV; my $in_file = shift @ARGV; my $out_file = shift @ARGV; my %code = (); my @aa = (); ...
written 6 days ago by JC9.1k
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Comment: C: Difference in R1 and R2 FASTQ files from RNA seq paired end
... The base call is performed independently, some sequencers remove low-quality reads without removing the respective pair, so you will end with singletons. ...
written 7 days ago by JC9.1k
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Answer: A: Linux sort P-values with scientific notation
... $ sort -g -k2 list A 1.14e-06 B 4.35e-05 C 0.5361 D 0.7278 ...
written 8 days ago by JC9.1k
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Comment: C: Converting amino acid sequences to numerical values
... this looks like a homework ... otherwise please explain why do you need the file in your research or offer to pay at least a coffee for a script ... ...
written 12 days ago by JC9.1k

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