Monday, 8 November 2010

Trimming adaptor seq in colorspace (SOLiD)

Needed to do research on small RNA seq using SOLiD.
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.. 

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