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Old 12-13-2018, 01:28 PM   #1
ritzriya
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Question 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.
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Old 12-17-2018, 08:18 AM   #2
ritzriya
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Old 12-17-2018, 11:25 PM   #3
luc
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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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Old 12-18-2018, 08:18 AM   #4
ritzriya
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Thank you luc.
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