When you run TOPHAT2 today, you see this record:
[2016-02-27 11:40:03] Checking for reference FASTA file warning:could not find FASTA file/home/pub/database/human/hg19/bowtie2_db/ hg19.fa.fa[2016-02-27 11:40:03] reconstituting reference FASTA file from Bowtie index executing:/home/pub/software /bowtie2/bowtie2-inspect/home/pub/database/human/hg19/bowtie2_db/hg19.fa >/home/xudl/mrna/15b1230a/data_ Analysis/map/tophat2/case2/tmp/hg19.fa.fa
TOPHAT2 the reference genome file with the name Bowtie2_index.fa is not found under the specified Bowtie2 index directory, the first step is based on
Bowtie2 index constructs the fasta sequence of the reference genome, using the Bowtie2-inspect program in Bowtie2
The program uses the following:
Bowtie2-inspect Bowtie2-inedx > Ref.fa
I have been using bowtie2 to do the right thing, I did not expect to have such a function.
Bowtie2-inspect Fasta sequence based on Bowtie2 index