PolyA Trimming

PolyA tails may be trimmed by including the settings --read-trimmers polya or --soft-read-trimmers polyg,polya. Polyg soft trimming is enabled by default.The minimum number of poly-A/poly-T bases required for trimming may be set using --trim-polya-min-trim. The default threshold is 20 poly-A/poly-T bases. Refer to Read Trimming for usage of read trimmers options.

The PolyA trimmer determines which end of the reads to trim for poly-A and poly-T sequences based on the library type. For example for Illumina forward stranded paired reads the trimmer will trim poly-A sequences at 3' end of read 1 and poly-T sequences at 5' end of read 2. If --rna-library-type is not provided or set to auto detect (A), the trimmer assumes the library is not stranded and trims poly-A sequences from 3' end of each read and poly-T sequences from 5' end of each read. The option --rna-library-type is described in Gene Expression Quantification.