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Using GISTIC 2.0 for Copy Number

29 Mart 2018 1.484 views Yorum Yok

GISTIC is one of the important tools in order to get the amplified or deleted regions in copy number variation data. You are giving the required information, and specifying the parameters (I generally preferred the default values), then it gives you the results. Installation is easy, you need to just follow the instructions in Install.txt in this folder.

If you cannot reach this ftp, and don’t have permission for copying files, then most probably you are using Safari; so try another browser 😉

If you follow the steps carefully, you will copy GISTIC_2_0_23.tar.gz into your folder. Then you will unzip Matlab Compiler Runtime (MCR). There is something that you need to pay attention. This installation file is for 64-bit Linux. If you have other machines, then you will download your own required MATLAB Compiler Runtime (MCR) version 8.3 (R2014a) into the same folder, then unzip it. If you complete your installation, then you can check the “run_gistic_example” and see that it works or not.

I am using TCGA copy number data, so I have updated example GISTIC run file as follows:

#!/bin/sh
## run example GISTIC analysis

## output directory
echo — creating output directory —
basedir=`pwd`/results
mkdir -p $basedir

echo — running GISTIC —
segfile=`pwd`/files/cnv_segment_file.txt
refgenefile=`pwd`/refgenefiles/hg38.mat
./gistic2 -b $basedir -seg $segfile -refgene $refgenefile

I have used hg38 because in my data’s pipeline it is used.I am not using optional files such as cnv file and marker file, and also I am not using parameters in here. In the example GISTIC run, they are showing some parameters that you can change:

# ./gistic2 -b $basedir -seg $segfile -mk $markersfile -refgene $refgenefile -alf $alf -cnv $cnvfile -genegistic 1 -smallmem 1 -broad 1 -brlen 0.5 -conf 0.90 -armpeel 1 -savegene 1 -gcm extreme

If you want to play with parameters, then you can look at this document for explanations:

ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm

That’s it! Enjoy your outputs!

If you have any question, just comment!

 

Additional Note:

I have faced this error while running a toy example:

Warning: Shortened … segments in ‘segmentation file.txt’ that overlap by one marker.

There is a solution here, maybe it works for you.

https://groups.google.com/a/broadinstitute.org/forum/#!topic/gistic-forum/Hab4gGEoUbQ

Bye again!

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