worker000000

thanks a lot, do you mean do as following? # umi_tools extract --bc-pattern=CNNNC --bc-pattern2=CNNNC --log=processed.log -I 28_1.fq.gz -S R1_TMP_umitools.fq.gz --read2-in=28_2.fq.gz --read2-out=R2_TMP_umitools.fq.gz # # delete cell_code and umi from fq2 zless...

can you have a look of my issuses in this https://github.com/CGATOxford/UMI-tools/issues/477 , thanks a lot

> Are you removing the UMIs in the FASTQ headers for read2? You do not need to do that. You only need to extract the UMI from the read sequences...

> When you pass in the `--paired` flag, any read1 that is removed will cause its corresponding read2 to be removed too. (Same behavior as UMI-tools) Thanks a lot fot...