bcl-convert and UMI's
0
0
Entering edit mode
8 weeks ago

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

bcl-convert UMI • 219 views
ADD COMMENT
0
Entering edit mode

none of these tools seem to be able to handle the output format from bcl-convert

Output from bcl-convert will be fastq files. Indexes can be in separate files if needed. Are you using a specific library kit?

ADD REPLY

Login before adding your answer.

Traffic: 3060 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6