UMI tools versus bcl2fastq2

[ritzriya]

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.

[ritzriya]

No reply yet?

[luc]

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.

[ritzriya]

Thank you luc.