Bioinformatics | TrimGalore를 이용하여 polyA제거하기

Trim Galore는 fastaq 리드 파일에서 adapter trimming과 quality trimming 할 수 있는 편리한 프로그램입니다.

adapter trimming 기능을 이용해서 polyA 서열 또한 제거를 할 수 있는데요, 옵션은 다음과 같습니다. 

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• -a/--adapter <STRING>

  • Adapter sequence to be trimmed. If not specified explicitly, Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used. Also see --illumina, --nextera and --small_rna.
  • If no adapter can be detected within the first 1 million sequences of the first file specified Trim Galore defaults to --illumina. A single base may also be given as e.g. -a A{10}, to be expanded to -a AAAAAAAAAA.

• -a2/--adapter2 <STRING>

  • Optional adapter sequence to be trimmed off read 2 of paired-end files. This option requires --paired to be specified as well. If the libraries to be trimmed are smallRNA then a2 will be set to the Illumina small RNA 5' adapter automatically (GATCGTCGGACT). A single base may also be given as e.g. -a2 A{10}, to be expanded to -a2 AAAAAAAAAA.

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