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cihga39871 / Atria

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
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Multiple adapter specifying #4

Closed asan-emirsaleh closed 2 years ago

asan-emirsaleh commented 2 years ago

Hello! Amazing job! Thank you a lot for you this tool to create!

I have a question on specifying multiple adapter. While doing round with --detect-adapter, the result would contain four strings for each direction. The are much shorter than default adapter sequences and several bases are different. Do I have to specify them all? How to specify multiple adapter seqs?

Best regards Asan

cihga39871 commented 2 years ago

Thank you for the question.

Usually, a sample only contains one adapter, so you can choose the adapter with the highest occurrence. We do not need to specify multiple adapters for one sample.

--detect-adapter only reports the first 16 bp of adapters, because

  1. Atria only detects the first 16 bp of adapters;
  2. the performance of any good trimmer does not change when using different adapter lengths (16-33). It is illustrated in the Atria Paper in Figure 4C: Figure 4C