LymphoTrack demultiplexing #1899
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You can run the preset as long as your FASTQs don’t contain multiple samples. So, if you have a pair of FASTQs for an IGH/IGL sample (Sample A) and another pair of FASTQs for a TRB/TRG sample (Sample B), you should run MiXCR using two separate commands. |
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The FASTQs do contain multiple samples - IGHV/IGK for sample A and TRB/TRG for sample B are all combined into one pair of FASTQs. Sorry if the wording was confusing. |
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Did you use any barcodes to separate the samples? |
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Hello! I'm analyzing data that was sequenced using the Invivoscribe LymphoTrack IGHV Leader, IGK, TRB, and TRG assay protocols. Amplicons from individual samples were pooled together after PCR amplification to generate the sequencing library.
Currently, I have a pair of FASTQ files with IGHV and IGK sequences from one sample and TRB and TRG sequences from a second sample. Can I simply run the built-in MiXCR presets for these assays or do I have to demultiplex further? Thank you!
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