Tophat with colorspace

[zorph]

I keep getting the following error even though I have designated -Q and -C in the command line. As you can see below:

tophat -C -Q -o /my/new/file /path/to/color_indexes/hg18_c /path/to/reads.cfasta /path/to/reads.quals

Any ideas for what might be wrong in my command line?

Error Message:

[Mon Nov 8 09:34:41 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Mon Nov 8 09:34:41 2010] Preparing output location /r/solid_xfer/Internal/AD/M_KOHLI/AD2/TopHat/
[Mon Nov 8 09:34:41 2010] Checking for Bowtie index files
[Mon Nov 8 09:34:41 2010] Checking for reference FASTA file
[Mon Nov 8 09:34:41 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Nov 8 09:34:41 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Mon Nov 8 09:37:25 2010] Checking reads
Error: file /r/solid_xfer/Internal/AD/M_KOHLI/AD2/reads/MartinAD_WT_AD2_AD6_20100402_solid0396_Martin_AD2_04pM_06pM_F3.csfasta does not appear to be a valid FASTA or FASTQ file

Error encountered parsing file /r/solid_xfer/Internal/AD/M_KOHLI/AD2/reads/MartinAD_WT_AD2_AD6_20100402_solid0396_Martin_AD2_04pM_06pM_F3.csfasta:
Records in Fastq files should start with '@' character

[mrawlins]

Try putting the quals file right between the -Q and -o switches.