Question: Problems with macs2
0
gravatar for anasofiamoreira94
9 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 • 431 views
ADD COMMENTlink modified 9 months ago • written 9 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 9 months ago by jared.andrews071.5k

Do you get an error?

ADD REPLYlink written 9 months ago by Devon Ryan86k

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

ADD REPLYlink written 9 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 9 months ago by genomax58k • written 9 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 9 months ago by Devon Ryan86k

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 9 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 9 months ago • written 9 months ago by ATpoint9.3k
0
gravatar for anasofiamoreira94
9 months ago by
anasofiamoreira9430 wrote:

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

ADD COMMENTlink written 9 months ago by anasofiamoreira9430
1

Please share the answer to help others in the future.

ADD REPLYlink written 9 months ago by ATpoint9.3k
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