Daniel:Notebook/GenomeMiner/2013-7-16: Difference between revisions

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[[Daniel:GenomeMiner|Back to Calendar]]
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]


Looked more into bowtie 2 format today.  Converted .txt files from Dr. Zhang which gave the raw sequences for the probes into .fa files using a MATLAB script I wrote.  Jeff informed me this is also easy on Python or Perl.  I plan on learning one of these (probably Perl) in order to do future endeavors, as it will not always necessarily be as easy to copy around files as I did this time.
Looked more into bowtie 2 format today.  Converted .txt files from Dr. Zhang which gave the raw sequences for the probes into .fa files using a MATLAB script I wrote.  Jeff informed me this is also easy on Python or Perl.  I plan on learning one of these (probably Perl) in order to do future endeavors, as it will not always necessarily be as easy to copy around files as I did this time.

Latest revision as of 22:55, 16 July 2013

Back to Calendar

Looked more into bowtie 2 format today. Converted .txt files from Dr. Zhang which gave the raw sequences for the probes into .fa files using a MATLAB script I wrote. Jeff informed me this is also easy on Python or Perl. I plan on learning one of these (probably Perl) in order to do future endeavors, as it will not always necessarily be as easy to copy around files as I did this time.

MATLAB script:


function [] = txt_to_fasta(input,set,outputname)
file=fopen(input);
M=textscan(file,'%s');
nprobe=length(M{1});
outfile=fopen(outputname,'w');
for i=1:nprobe
fprintf(outfile,'>Probe_set%i_%i\n',set,i);
fprintf(outfile,'%s\n',M{1}{i});
end