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  • UMI tools versus bcl2fastq2

    Hi All,

    I just found out that bcl2fastq2 also handles adapter trimming and UMI extraction right at the level of basecall to fastq conversion. If that is available, why would anyone use UMI_tools software?

    Also, if we used bcl2fastq2 in the right way, is there a need to deduplicate using Picard or UMI_tools post alignment?

    Please share your experience as I am new to UMI processing. (Illumina NextSeq 500 miRNA single-end reads of length 75 bp)

    Thank you,
    Ritzriya.

  • #2
    No reply yet?

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    • #3
      bcl2fastq will only transfer the UMI information into the read header and trim them out of the reads as an option - nothing else.
      UMI-tools are more sophisticated and have many additional functions.

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      • #4
        Thank you luc.

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