TopHat error!

[Fuyou Fu]

Hi,

When I run Tophat, I have this error files. Could anybody tell me how  to handle it?

Thanks,

Fuyou

[2015-01-05 09:48:25] Beginning TopHat run (v2.0.13)

-----------------------------------------------

[2015-01-05 09:48:25] Checking for Bowtie

 Bowtie version: 2.2.4.0

[2015-01-05 09:48:26] Checking for Bowtie index files (genome)..

[2015-01-05 09:48:26] Checking for reference FASTA file

[2015-01-05 09:48:26] Generating SAM header for ref/Striga

[2015-01-05 09:48:28] Reading known junctions from GTF file

[2015-01-05 09:48:30] Preparing reads

left reads: min. length=30, max. length=101, 8733918 kept reads (706 discarded)

right reads: min. length=30, max. length=101, 8732626 kept reads (1998 discarded)

[2015-01-05 09:53:30] Building transcriptome data files str-1/tmp/StrigaC

[2015-01-05 09:53:32] Building Bowtie index from StrigaC.fa

[FAILED]

Error: Couldn't build bowtie index with err = 1

[Nathan Johnson]

You need to build a bowtie index file for Tophat to use.  I suggest reading through the Tophat manual to go through the steps on how to make them.