Errors coming up in filtered SOLiD csfasta reads after using SOLiD_preprocess_filter_v2.pl

Question

[zainab12khanum]

Hello, I am a beginner in Transcriptomic analysis.I am using SOLiD 5500 platform and have sequenced short fragment reads.I first converted the XSQ format in to csfasta and Qual and then used the SOLiD_preprocess_filter_v2.pl script for Pre-processing of these files. The script I used was:

 perl SOLiD_preprocess_filter_v2.pl -i f -f [path for csfasta file] -g [path for Qual file] -o [output directory name]

All the filtered reads in Filtered-T- files still had dots in the start, middle and in the end. We can not use this data to run SATRAP assembler as Oases will not encode the dots. Please guide us and provide us with the scripts to get right results. Also please advice us that are we leaving out some parameters in this SOLiD_preprocess_filter_v2.pl script? Thank you.