Problems with macs2
Good afternoon, I'm working with data from ChIP-seq and now i'm using MACS2 Callpeak, however it only runs to one sample not for the other two. Did this happen to anyone? I don't understand why it only works to one sample. Thanks.
• 1,683 views
•
link
written
by
anasofiamoreira94
1 answer
I've realized what was the problem, thank you so much for the help.
• 0 views
•
link
written
by
anasofiamoreira94
Log in to answer this question.
More posts like this
-
MACS2 not working in paired end mode
written by Filago •
-
Macs2 tmp directory
written by KH •
-
MACS2 and single file for analysis
written by Morris_Chair
-
MACS2: Missing Peaks in Bed file but Present in Bedgraph/Bigwig?
written by Ankit
-
Identifying differential histone mark (H3k27me3 and H3k4me3) in treated and control sample
written by munaj86 •
-
Merging fastq files
written by william.mcentegart •
-
Using MACS2 for peak calling
written by anais1396 •
-
ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
written by shawn.w.foley
-
Difference Between PolyA and Hybrid Selection for RNA-Seq
written by adamlangenbucher •
-
MACS2 bdgcmp for two bedgraph peak calling
written by BIOTIN •
Do you get an error?
No, in the end, the report doesn't give me an error
How are you calling the command? Posting your actual code will help us troubleshoot. It's hard to help with so little info.
I'm so sorry, here is my code to one of the samples:
So does it just not finish ever or what? I've actually seen that happen on occasion, never figured out why though.
No it finishes, it does the peaks to one of the samples, and to the other ones, creates the files of the output without the peaks.
Are all the output files for this sample empty? Can you post the log that macs prints to stderr?
Hello anasofiamoreira94!
We believe that this post does not fit the main topic of this site.
Closed, problem solved by OP
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!