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Old 02-16-2010, 07:29 AM   #1
Location: Taiwan

Join Date: Jan 2010
Posts: 17
Default Tophat and Bowtie

I know that Tophat would call bowtie to form fasta(*.fa) files as references.
And I use the command as follows:
./tophat -r 5 -p 12 chr22 ../TestData/s_1_1_seq.txt ../TestData/s_1_2_seq.txt

All the process is running well, but I figure out that tophat would call bowtie.
However, I already have chr22.fa in the current folder.
And I also have chr22.*.ebwt files in the current folder.

What's wrong?
What is bowtie doing now?

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