tophat2 transcriptome data files created

[konika]

Hi I am providing tophat with pre-built bowtie index files, Gff files and the whole genome fasta file, but it still creates transcriptome data files and is building bowtie indexes. Is it necessary, as it takes a long time.
The command i use
tophat2 -G /home/chawla/rna_seq_pipeline/gff/mouse_ensembl.gff /home/chawla/rna_seq_pipeline/gff/mouse_ensembl /home/chawla/rna_seq_pipeline/trunk/processed/shNuak1-D704_S4_L001_R1_001_sample.trimmed.gz


the run :
[2015-08-11 14:43:26] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2015-08-11 14:43:26] Checking for Bowtie
Bowtie version: 2.1.0.0
[2015-08-11 14:43:26] Checking for Samtools
Samtools version: 0.1.18.0
[2015-08-11 14:43:26] Checking for Bowtie index files
[2015-08-11 14:43:26] Checking for reference FASTA file
[2015-08-11 14:43:26] Generating SAM header for /home/chawla/rna_seq_pipeline/gff/mouse_ensembl
format: fastq
quality scale: phred33 (default)
[2015-08-11 14:44:01] Reading known junctions from GTF file
[2015-08-11 14:44:41] Preparing reads
left reads: min. length=84, max. length=84, 8251 kept reads (4 discarded)
[2015-08-11 14:44:41] Creating transcriptome data files..
[2015-08-11 14:46:28] Building Bowtie index from mouse_ensembl.fa


i dont understand the need, kindly help.

[GenoMax]

Refer to the solution that was provided to your query in this thread: http://seqanswers.com/forums/showthread.php?t=46731