UMI tools versus bcl2fastq2

ritzriya

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#1

UMI tools versus bcl2fastq2

12-13-2018, 01:28 PM

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.
Tags: bcl2fastq2, illumina nextseq, umi-tools
ritzriya

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#2

12-17-2018, 08:18 AM

No reply yet?
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luc

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#3

12-17-2018, 11:25 PM

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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ritzriya

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#4

12-18-2018, 08:18 AM

Thank you luc.
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UMI tools versus bcl2fastq2

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