tophat-bowtie building index

[repinementer]

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TopHat also requires a fasta file (.fa) for your reference. If this file is not found alongside the other index files, the program will use the Bowtie index you give it to build this file and save it to the output directory. This step can take up to an hour for a human-sized genome. To skip this step in future runs, you can move the fasta file from the tophat_out directory to the directory containing the Bowtie index files.
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I downloaded hg18 zip file and unzipped it as per instruct..
After running make_hg18.sh script all I can see is the following list (ch1. fa to chrY.fa and other .ebwt files) but I couldn't see any human.fa reference file in ./tophat_out folder.

Do i need to merge all individual .fa files into a single file ???

like
cat chr1.fa chr2.fa......chry.fa >>human.fa ?????

[john_mu]

Yes that is how TopHat works, you need to merge all the files.

You should call it "genome.fa"

EDIT: also, if you did not merge them, TopHat will generate one using "bowtie-inspect" and save it in the tophat_out folder. If you did not see one, something went wrong.