TopHat Error: you must set the mean inner distance between mates with -r?

[xhuister]

I tried to use TOPHAT on Arabidopsis mRNA-seqs, they are not pair end reads. I've run the example data you provided, so the installation is all right.
For my own data, I've built bowtie index "tair9_bwt" for Arabidopsis genome sequences. I have 6 fastq files of mRNA-seqs. I want to use TOPHAT to find new transcript boundaries in intergenic regions.

I used the following command to test two of the six fq files, it could generate the 3 output files successfully.
tophat ~/bowtie-0.12.5/tair9_bwt/tair9_bwt tail.fastq,test1.fastq

But when I tried to use options like -i -I or -G or other options, it failed:
-----------------------
$ tophat ~/bowtie-0.12.5/tair9_bwt/tair9_bwt tail.fastq,test1.fastq -i 30 -I 15000
Error: you must set the mean inner distance between mates with -r
Traceback (most recent call last):
File "/home/wux3/mrnaseq/tophat/bin/tophat", line 1635, in ?
sys.exit(main())
File "/home/wux3/mrnaseq/tophat/bin/tophat", line 1535, in main
exit(1)
TypeError: 'str' object is not callable
----------------------

The description of -r option is:
-r/--mate-inner-dist <int> This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs.

But the mRNA-seqs I have are not paired end, anybody knows how to set this option on my data? And, why the "-r" option is not neccessary when no options used in the commandline?

Thank you in advance.

[xhuister]

Now, it is OK. Just used options before the fastq... -.-

tophat -G TAIR9_GFF3_tophat -i 30 -I 15000 ~/bowtie-0.12.5/tair9_bwt/tair9_bwt tail.fastq,head.fastq

[maximilianh]

thanks for posting this, just saved me a lot of frustrations...