Hi, after getting sam file from Bowtie2, I convert it to sorted.bam and then index it according to UMI-tools documention. Seems all are fine, but, when I run umi_tools dedup with the following command, nothing is written in the output file. I had removed the '--output-stats' command to make it faster.
command: umi_tools dedup -I example.bam -S deduplicated.bam
However, before running my final dataset, I had checked with a sample dataset, it that case it was working. Do you have any idea, please? Thanks.