...
- If you have a
mappingdirectory with output from the Mapping tutorial or and the SNV calling tutorial, then you should use those files for part 1 of this tutorial. You can proceed with either one alone or with both. Expand title If you have not done the other tutorials and want a "canned" data set provided for you, click here for example files. Code Block $BI/gva_course/mapping/IGV # location of example files cp -r /corral-repl/utexas/BioITeam/gva_course/mapping/IGV . # example command to copy to current directoryscp -r username@lonestar.tacc.utexas.edu:/corral-repl/utexas/BioITeam/gva_course/mapping/IGV . # to copy to a local computer skipping the step of copying to a lonestar directory and secure copying from there.
Then skip down to #Launching IGV.
...
IGV likes its reference genome files in GFF (Gene Feature Format). Unfortunately, our old friend bp_seqconvert.pl doesn't do GFF. So, we're going to show you another tool for sequence format conversion called Readseq. We've already installed it into the $BI/bin directory so you don't have to, but here we provide the steps that can be used to install it in a local directory.
| Expand | ||
|---|---|---|
| ||
To use it you need to first download the file readseq.jar linked from here. To get this onto TACC easily, use:
|
...
To do the conversion that we want, use this command:
| Code Block |
|---|
java -cp /corral-repl/utexas/BioITeam/bin/readseq.jar run NC_012967.1.gbk -f GFF -o NC_012967.1.gbk.gff
|
...
The easiest way to to this is probably to copy everything you want to transfer into a new directory called IGV. Since many of the tutorial output files had the same names (but resided in different directories) be careful to give them unique destination names when you copy them into the new directory together. To ensure you don't overwrite things be sure to use the -n command on the cp option.
For starters, you could change into your mapping directory and run commands like these if you just came from the mapping tutorial:
...