Question: Problems with macs2
0
gravatar for anasofiamoreira94
10 days ago by
anasofiamoreira940 wrote:

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.

chip-seq • 151 views
ADD COMMENTlink modified 7 days ago • written 10 days ago by anasofiamoreira940
1

How are you calling the command? Posting your actual code will help us troubleshoot. It's hard to help with so little info.

ADD REPLYlink written 10 days ago by jared.andrews07640

Do you get an error?

ADD REPLYlink written 10 days ago by Devon Ryan76k

No, in the end, the report doesn't give me an error

ADD REPLYlink written 8 days ago by anasofiamoreira940

I'm so sorry, here is my code to one of the samples:

srun shifter macs2 callpeak -t uCas1_n1.bam -c uEmp_n1.bam -f BAM -g mm -n uCas_n1_VS_uEmp_n1_peakCal -q 0.05 -s 40
ADD REPLYlink modified 8 days ago by GenoMax42k • written 8 days ago by anasofiamoreira940

So does it just not finish ever or what? I've actually seen that happen on occasion, never figured out why though.

ADD REPLYlink written 8 days ago by Devon Ryan76k

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.

ADD REPLYlink written 8 days ago by anasofiamoreira940

Are all the output files for this sample empty? Can you post the log that macs prints to stderr?

ADD REPLYlink modified 8 days ago • written 8 days ago by ATPoint3.0k
0
gravatar for anasofiamoreira94
7 days ago by
anasofiamoreira940 wrote:

I've realized what was the problem, thank you so much for the help.

ADD COMMENTlink written 7 days ago by anasofiamoreira940
1

Please share the answer to help others in the future.

ADD REPLYlink written 7 days ago by ATPoint3.0k
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