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  • Mismatch Issue with Analysis of direct cDNA data

    Hello,

    I have used oxford nanopore's direct cDNA sequencing kit to obtain transcript information from 18 different samples. Right now I am trying to run a differential expression analysis between 6 of them as set up below:

    sample_id condition
    barcode01 untreated
    barcode02 untreated
    barcode03 untreated
    barcode10 treated
    barcode11 treated
    barcode12 treated

    When I run the differential expression analysis pipeline it gives me the following error:
    • Join mismatch for the following entries:
    • - key= values=[],[],[],[],[],[]
    • - key=barcode02 values=[/mnt/c/Users/topas/epi2melabs/instances/wf-transcriptomes_eeff4573-1a2e-4ebc-976c-fd1466292ea2/work/7d/8eeebc22ec390d2c71666b1ac5f05d/barcode02.fastq]
    This error repeats for all of my samples. I have checked the names and they are the same on the TSV as the files themselves. Does anyone know what might be causing this error?

    Thank you!

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