Entering edit mode
2.3 years ago
matthias.desmet
▴
30
Hi,
We're looking into using bcl-convert
as an alternative for Picard
wrt "UMI aware" demultiplexing.
Picard can demultiplex straight to bam with the UMI in the correct RX
tag. bcl-convert appends the UMI sequence to the fastq header line when using the OverrideCycles
option.
I'm looking for a way to get the UMI sequence from the fastq header into the sam RX
tag (with or without alignment). I've already looked into fgbio, umi-tools, umis; but none of these tools seem to be able to handle the output format from bcl-convert
.
Does anyone have a suggestion?
Thanks M
Output from
bcl-convert
will be fastq files. Indexes can be in separate files if needed. Are you using a specific library kit?