Daniel:Notebook/GenomeMiner/2013-7-16: Difference between revisions
Jump to navigation
Jump to search
>Djacobse No edit summary |
>Djacobse No edit summary |
||
Line 1: | Line 1: | ||
[[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
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