I'm dealing with HGS data generated by SOLiD 3 sequencing data, and in the pre-processing step, I want to find the contamination reads from the sequencing data. But since the data is in color-space form, I can't find a software to make the function.(Some softwares such as SeqTrim are designed for 454&Illumina platform). So did anyone meet with the same problem? How can I deal with the color-space data about contamination or artifacts?
what do you mean by contamination? DNA from a different genome?
plz define the "contamination", if you are referring to primer, rRNA(in RNA-seq) and barcodes, these could easily be filtered-out in the Bioscope filter step
Thanks for your answer, mainly I'm considering sequences from adaptors (primer?) and vector contamination now, we used MNase-seq to generate the data from human nucleosomes, so there is no rRNA and barcodes in the datasets. In this situation, can I use the software you recommended?
Yes, vector contamination and sequences from adaptors