macs does work for histone modifications, but you have to specify --nomodel. also specify --nolambda if you don't have control data.
they have a workflow in their new publication: http://goo.gl/5HQlO
-
hi.
what you mean by "peaks donot match"? match what?
are you sure your primary/raw data is any good? what do your eyes tell you when you browse the coverage tracks in a genome browser, do you see an expected pattern?
anyway there are many tools out, none of which has really been tested on a reference dataset that has been independently confirmed with a different technology (afaik). therefore there is no 'best' tool for everybodies dataset.
i personally would tend to recommend SICER as histone modifications are not necessarily found to have peak-shaped enrichment patterns.Leave a comment:
-
ChIP seq packages for histone modification data
Hi all,
Which chip seq peak calling algorithm would you suggest to be the best for histone modification data such as H3k4me3, H3k9me3 etc in terms of usage and accuracy.
I am trying to use MACS and cis genome. The peaks donot match (even 10%).
-
This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...03-03-2025, 01:39 PM -
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM
Leave a comment: