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FrickTobias / BLR

MIT License
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10x integration only for EMA at the moment #216

Closed pontushojer closed 4 years ago

pontushojer commented 4 years ago

Currently read in the 10x version of the pipe are only outputted in the EMA mapper format. Meaning that they are:

  1. split into non-barcoded and barcoded FASTQs
  2. have headers in the format @ST-E00273:177:HMTTCCCXX:1:1101:5457:6407 BX:Z:CAAGTTGTCCGAAGAG-1

They are also sorted which means that the sorting step should not be applied.

For them to be compatible with the other mappers we need to:

  1. Merge non-barcoded and barcoded FASTQs.
  2. Reformat headers in the style: @ST-E00273:177:HMTTCCCXX:1:1101:5457:6407_BX:Z:CAAGTTGTCCGAAGAG-1 (connect BX through hyphen "-")