KeyError: 'TN' Error with TopHat on SOLiD data

[jaldrich]

Hi -

I'm getting this error from TopHat when trying to run Paired-end RNA-seq data (50mer and 35mer).

File "/home/jaldrich/tophat-1.1.4.Linux_x86_64/tophat", line 1520, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: 'TN'

I get the same error if I use the CSFASTA/QUAL file straight from the sequencer with no modifications and if I use modified CSFASTA/QUAL files where the . has been replaced with N (CSFASTA file) and the -1 has been replaced with a 1 (QUAL file).

I'm using TopHat v1.1.4 and bowtie version 0.12.7.

Any suggestions?

Thanks!