Haowen Zhang

It seems that you are mapping single-end bulk ATAC-seq data? Can you provide more details on your data? Why is it single-end ATAC-seq? And how long are the reads?

I think usually people get paired-end reads for ATAC-seq. I recall Bowtie2 very sensitive mode just sample more seeds and maybe tolerate more errors in the reads, which makes it...

@mourisl Is this way of using read-format supported?

The manpage is at https://haowenz.github.io/chromap/chromap.html

I see the issue. It should work with low memory mode turned off. In this case, the temp mapping files won't be generated. Otherwise, it will generate temp mapping file...