Wasn't clear of the adaptor trimming procedure (its dead easy in basespace fastq files but oh well, SOLiD has directionality and read lengths dont' really matter for small RNA)
novoalign suggests the use of cutadapt as a colorspace adaptor trimming tool
was going to script one in python if it didn't exist
Check their wiki page
Sadly on CentOS I most probably will get this
If you get this error:
File "./cutadapt", line 62 print("# There are %7d sequences in this data set." % stats.n, file=outfile) ^ SyntaxError: invalid syntax
Then your Python is too old. At least Python 2.6 is needed for cutadapt.
have to dig up how to have two versions of Python on a CentOS box..