I've got ATAC-seq fragments file I downloaded from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4156599
It doesn't have an index, so I figured I'd create one with tabix. The first error I got was:
[tabix] the compression of 'GSM4156599_brain.atac.fragments.bed.gz' is not BGZF
I fixed that by uncompressing and running bgzip. Now when I run
tabix -p bed GSM4156599_brain.atac.fragments.bed.gz
the output is:
[E::hts_idx_push] Unsorted positions on sequence #1: 3107211 followed by 3107198
tbx_index_build failed: GSM4156599_brain.atac.fragments.bed.gz
I've attached the file https://drive.google.com/file/d/1WkDqWpRQlaEPeiSbChYZCIbSIzVFJ0FX/view?usp=sharing Does something about this bed seem off to you?
Thanks in advance!