Talk:Wikiomics:EMBO Tunis 1: Difference between revisions
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Darek Kedra (talk | contribs) (New page: =Exercises 17th Sep 2014 afternoon= This part is meant to be with an active participation of students (& teacher), therefore resembling a bit more real life situations where working direct...) |
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cp -i /path/to/desired/file . | cp -i /path/to/desired/file . | ||
</pre> | </pre> | ||
If you feel stranded unix command line wise, try checking this tutorial: | |||
http://openwetware.org/wiki/Wikiomics:WinterSchool_day1#Introduction_to_Linux_and_the_command_line | |||
==Starting== | ==Starting== | ||
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Lets go there: | Lets go there: | ||
<pre> | <pre> | ||
#jump to home directory if you happen to be somewhere else | #jump to home directory if you happen to be somewhere else | ||
| Line 37: | Line 41: | ||
ls -R | less | ls -R | less | ||
press q if you need to quit | press q if you need to quit | ||
</pre> | |||
==Configure new genome to use in IGV== | |||
<pre> | |||
#go to dir with required files | |||
cd 000_igv | |||
#see what is there in one column | |||
ls -1 | |||
</pre> | </pre> | ||
Revision as of 03:00, 17 September 2014
Exercises 17th Sep 2014 afternoon
This part is meant to be with an active participation of students (& teacher), therefore resembling a bit more real life situations where working directories do not contain all files needed at the given step.
You should either create symbolic links
ln -s /path/to/desired/file . #or copy them cp -i /path/to/desired/file .
If you feel stranded unix command line wise, try checking this tutorial: http://openwetware.org/wiki/Wikiomics:WinterSchool_day1#Introduction_to_Linux_and_the_command_line
Starting
there will be 0917_kd directory in which you will find a set of subdirectories:
000_igv 00_fasta 01_fastq 02_sambam 03_gtf 04_bed 05_vcf 06_wig 07_bwa 08_last 09_last_genomes
Lets go there:
#jump to home directory if you happen to be somewhere else cd #go to this directory cd 0917_kd #list the content ls ls -R | less press q if you need to quit
Configure new genome to use in IGV
#go to dir with required files cd 000_igv #see what is there in one column ls -1
