The GAPipeline-1.0 was used starting from the IPAR-1.01 calculated intensities. First the data sets are screened for the sequence of the 5' adapter (We sometime observed that parts of the 5' adapter can be cloned instead of a small RNA insert) with the same method than described below using the last 10 bases of this adapter. This was not observed for your samples so all reads were processed for the 3prime adapter location and removal. The adapter sequences were trimmed in 3 steps: 1) The 21nt adapter sequence is used, which permits to identify “inserts” of 15nt or less. 2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 6 bases permits identifying inserts of up to 30 bases. 3) Finally the remaining reads are search for notexact matches of the adapter. The first 4 bases of the adapter were searched within the full reads sequences and at least 75% of the following bases must be identical to the adapter sequence (max 31 bp).
