Question: Problems with macs2
0
gravatar for anasofiamoreira94
12 months ago by
anasofiamoreira9430 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 • 480 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by anasofiamoreira9430
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 12 months ago by jared.andrews071.8k

Do you get an error?

ADD REPLYlink written 12 months ago by Devon Ryan88k

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

ADD REPLYlink written 12 months ago by anasofiamoreira9430

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 12 months ago by genomax62k • written 12 months ago by anasofiamoreira9430

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 12 months ago by Devon Ryan88k

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 12 months ago by anasofiamoreira9430

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

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint13k
0
gravatar for anasofiamoreira94
12 months ago by
anasofiamoreira9430 wrote:

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

ADD COMMENTlink written 12 months ago by anasofiamoreira9430
1

Please share the answer to help others in the future.

ADD REPLYlink written 12 months ago by ATpoint13k
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