paired-end reads where UMI is located in read 2

[silvia1234567890]

Hello,

Can I use UMI-tools to analyse paired-end sequencing reads where UMI is located at the beginning of read 2?

Thank you!

[IanSudbery]

Sure. Just provide read 2 to --stdin (or on the pipe) and provide read 1 to --read2-in.

[silvia1234567890]

I mean, only in read 2, not in read 1 (just to confirm, thank you)

[IanSudbery]

Yep,

$umi_tools extract --stdin=read2.fastq.gz --stdout=read2.processed.fastq.gz --read2-in=read1.fastq.gz --read2-out=read1.processed.fastq.gz --bc-pattern=NNNNNN

Will take a UMI off the start of read2 and add it to the read name of both read1 and read2.

[silvia1234567890]

and what type of information can I obtain with UMItools when I have end-paired sequencing reads where UMI is located in read 2 only?

Thank you so much for your help, best regards

[TomSmithCGAT]

Closing due to inactivity.