STAR demo for beginners

This is the demo STAR for beginners to make it easy for beginners to use STAR.

How to download and run demo STAR? (For Linux/Mac user)

Step 0, before you run this demo, you are supposed to have git to download the source code.

• Please type git and run in the terminal to check whether you have installed the git. If not, the terminal will show you the one-line code to install git.

• You can also use other command to download the source code in this page. However, you may meet with the permission and software safety problems when using other methods to download the source code. If you come up with such problems in Mac, you should go to system perferences/Security & Privacy option to allow the software.

Step 1, clone this demo respository, run

git clone https://github.com/jligm-hash/demoSTAR

• After this step, you will see demo folder is inside the demoSTAR folder. Inside demo folder, there are data folder, result folder, linuxOS folder, macOS folder, starLinux.sh, starMac.sh.

Step 2, download the genome folder we prepared for you and copy the genome folder (including the files in it) into the data folder.

• After this step (downloading the files in genome folder), there should be genome folder, RNAseq folder and result folder inside the data folder. The important files for your running should inside genome folder and they are Genome, chrLength.txt, geneInfo.tab, chrName.txt, genomeParameters.txt, SA, chrNameLength.txt, sjdbInfo.txt, SAindex, chrStart.txt, sjdbList.fromGTF.out.tab, chr21.hg37.fa, exonGeTrInfo.tab, sjdbList.out.tab, chr21.hg37.gtf, exonInfo.tab, transcriptInfo.tab.

• Pay attention to the name of genome folder. If its name is not genome, you may get the error and need to reverse the genome folder name in starLinux.sh or starMac.sh.

• As an alternative, you can generate the genome folder instead of downloading and setting the directory of them. Just try to run the script genomeLinux.sh or genomeMac.sh in the command (in the working directory of ./demo). Once you have run it successfully for one time, you don't have to run it every time.

Step 3, make sure you change the working directory to ./demo, for example, you may run

cd ./demoSTAR/demo

Step 4, start running demo STAR

For linux user, run bash starLinux.sh or ./starLinux.sh

For Mac user, run bash starMac.sh or ./starMac.sh

Step 5, check your results in result folder.

Notes

• For the demo STAR running, the memory (or RAM) more than 6GB is recommended.

• For original released information on STAR, please turn to STAR.