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Question: Output Files of MACS2 bdgdiff
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gravatar for hamza_karakurt
6 months ago by
hamza_karakurt • 10
hamza_karakurt • 10 wrote:

Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each condition) and I used BDGDiff tool to find differential peaks. It needs 4 bedgraph files so I gave 2 replicates for 2 conditions and now I have 3 out files in bed format, Condition 1 (19,960 regions), Condition 2 (0 regions) and common (230 regions).

Which one of them have differential peaks and how can I extract gene names from these bed files?

Thank you.
bedgraph bed macs2 chip-seq • 334 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by hamza_karakurt • 10
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool compares peaks between conditions and outputs those unique to each and those in common. From the tool author's help: https://github.com/taoliu/MACS/wiki/Call-differential-binding-events

Three types of differential regions will be reported: 1. those having more enrichment in condition 1 over condition 2 ( cond1_ChIP > cond1_Control and cond1_ChIP > cond2_ChIP ); 2. those having more enrichment in condition 2 over condition 1 ( cond2_ChIP > cond2_Control and cond2_ChIP > cond1_ChIP ); those having similar enrichment in both conditions ( cond1_ChIP > cond1_Control and cond2_ChIP > cond2_Control and cond1_ChIP ≈ cond1_ChIP ).

There are other tools that you can experiment with if this is not exactly the data you want to evaluate. Please see the Galaxy ChIP-seq tutorials here for examples: https://galaxyproject.org/learn/

Coordinates in BED/interval datasets can be compared to link in gene/transcript annotation. Obtain or create a BED dataset with the gene/transcript name in the 4th field ("name") and compare it to your peaks. Examples of joining data based on coordinate overlap are in the Galaxy 101 tutorial (included in the same tutorial link above).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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