Adapter stripping and read length limit

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Array Studio aligns the adapter sequence against read sequence to strip up to where the best alignment to the adapter ends. Array studio strips reads from 3’end strictly when the overlap between adapter sequence and read is less than 7 bp. If the overlapping length > 7bp, then mismatches are allowed if the quality of the mismatch position is low.

The read is stripped based on the starting location of the best alignment.

The stripping is aggressive because 1-2 bp of adapter sequence may results in calling of mismatches in alignment.

The minimal length required for the read after adapter stripping is 17bp for alignment step. Array Studio keeps both reads in a pair even if one of the reads is shorter than 17bp after stripping. e.g. Paired end reads, R1 and R2, have read length 75 and 7bp, respectively, after trimming and adapter stripping. If we keep R1 in the filtered fastq file, we have to keep R2 too, to maintain the line order, 1-1 line matching of PE files.