Trimming Read Length of 10X Output

For scRNAseq, 10x recommends using a 150 Cycle High Output Kit, but many experiments will work with the less expensive 75 Cycle High Output Kit. These instructions show you how to trim read length from a 150 Cycle run to simulate output with a 75 Cycle Kit and determine if you can use this kit for future sequencing runs.

  1. Navigate to the folder containing your BCL files.
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  3. The file you need is RunInfo.xml. I would create a copy of this file as a backup with a different name (e.g. RunInfoOriginal.xml). This file is part of how the sequencer decides on the read lengths when processing BCL files. CellRanger also uses this file to decide how long each read should be when it makes fastqs.
  4. When you look at the file, the first few lines contain a lot of the info you supplied when you set up the run. In particular you can see the read number 3 has 91 cycles, which is your mRNA read.
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  6. So, simply change this from 91 to 56 and save the file as RunInfo.xml (do not change the name!). Now the cycles should match how you’d normally set up a 75-cycle run on the sequencer.
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  8. Run CellRanger as normal.