Low read coverage in Input: Peak calling/Filtering
0
0
Entering edit mode
6 weeks ago
Ankit ▴ 320

Hi everyone,

I have a datasets where the coverage of input is relatively. Actually many reads were filtered out during deduplication step. When I performed peak calling, though peaks are called but low input coverage put me in doubt as if they are reliable or not.

One way I filtered out the peaks with low read count after counting. But since my interest is heterozygosity inside input reads the counting does not help. I also tried to call heterozygous bases from Input but then it is a round-about way to deal.

Is there any other way I can control number of reads in input to consider for peak calling?

Or can I merge both replicates of input to use as merged input (so I use same input for replicates of ChIP)?

Or we need more sequencing done for input to increase coverage (matter of cost)?

I am using MACS1/MACS2 for peak calling.

I would appreciate any suggestions.

Thank you

reads peaks chip-seq • 103 views
ADD COMMENT

Login before adding your answer.

Traffic: 2183 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6