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tutorials:eccb_t2_tdg09 [2012/09/06 21:16] romainstuder |
tutorials:eccb_t2_tdg09 [2012/09/08 16:26] (current) romainstuder |
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| Download from here: | Download from here: | ||
| + | [[http://www.homepages.ucl.ac.uk/~ucbtaut/]] | ||
| + | [[http://bit.ly/fVbnDr]] => tdg09.zip | ||
| + | <code> | ||
| + | unzip tdg09.zip | ||
| + | </code> | ||
| + | |||
| + | === Detection of site in the Influenza Virus Hemagglutinin HA1 chain === | ||
| - | === Detection of site in the Influenza Virus (NOTE!!!) === | + | We would like to know which sites are important between the Hemagglutinin HA1 of the virus in Avian (genes starting with Av_) and in Human (genes starting with Hu_). |
| <code>cd ./Tutorial/tdg09 # Folder of installation</code> | <code>cd ./Tutorial/tdg09 # Folder of installation</code> | ||
| Line 23: | Line 30: | ||
| The output is put in the file tdg.out. | The output is put in the file tdg.out. | ||
| - | We need to transform it with some unix tools: | + | We need to transform it with some unix tools (the four lines are one unique command): |
| + | (/!\ These Unix tools need Cygwin to work in Windows /!\ If you don't have Cygwin, you can continue the tutorial by skip the R part. The sites are given at the end). | ||
| <code> | <code> | ||
| - | grep "Site\|Parameters\|Log\-likelihood" tdg.out | tr '\n' ' ' | sed "s/Site: /\\`echo -e '\n\r'`/g" | awk '{$1=$1}1' OFS=" " | cut -d' ' -f1,4,7,10,13 > tdg2.out | + | grep "Site\|Parameters\|Log\-likelihood" tdg.out \ |
| + | | tr '\n' ' ' | sed "s/Site: /\\`echo -e '\n\r'`/g" \ | ||
| + | | awk '{$1=$1}1' OFS=" " \ | ||
| + | | cut -d' ' -f1,4,7,10,13 > tdg2.out | ||
| </code> | </code> | ||
| Line 57: | Line 68: | ||
| Put a vertical line a the root of the tree to split the tree in two. | Put a vertical line a the root of the tree to split the tree in two. | ||
| - | => Visualise the position of these sites | + | => Visualise the position of these sites. |
