DiffBind Chip-Seq error

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1

Hi,
I have Chipseq data and 2 replicates for each condition. I did MACS2 peak calling and tried to perform DiffBind. But I always get the same error. [1] “en_US.UTF-8”

Can you please help me with this.
Thanks

2

Hi @dush,
could you provide additional information about the error report? You can find it in the bug icon:

Regards

3

Detailed Job InformationJob environment and execution information is available at the job info page.

Job ID | 36606423 (bbd44e69cb8906b530f67995209c8a3a) |

Job Execution and Failure Information#### Command Line

ln -s '/galaxy-repl/main/files/057/429/dataset_57429239.dat' 'Treated-MACS2_callpeak_on_T-peaks.bed' &&   ln -s '/galaxy-repl/main/files/057/429/dataset_57429110.dat' 'Filter_SAM_or_BAM__T-bamreads.bam' && ln -s '/galaxy-repl/main/files/_metadata_files/004/628/metadata_4628948.dat' 'Filter_SAM_or_BAM__T-bamreads.bai' &&      ln -s '/galaxy-repl/main/files/057/429/dataset_57429139.dat' 'Filter_SAM_or_BAM__N-bamcontrol.bam' && ln -s '/galaxy-repl/main/files/_metadata_files/004/628/metadata_4628955.dat' 'Filter_SAM_or_BAM__N-bamcontrol.bai' &&      ln -s '/galaxy-repl/main/files/057/429/dataset_57429192.dat' 'Control-MACS2_callpeak_control62121_narrow_Peaks-peaks.bed' &&   ln -s '/galaxy-repl/main/files/057/429/dataset_57429080.dat' 'Filter_SAM_or_BAM__C-bamreads.bam' && ln -s '/galaxy-repl/main/files/_metadata_files/004/628/metadata_4628952.dat' 'Filter_SAM_or_BAM__C-bamreads.bai' &&              Rscript '/cvmfs/[main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/194e3f2c1d86/diffbind/diffbind.R](http://main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/194e3f2c1d86/diffbind/diffbind.R)'  -i '[["Condition", [{"Control": ["Filter_SAM_or_BAM__N-bamcontrol.bam"]}, {"Control": ["Filter_SAM_or_BAM__C-bamreads.bam"]}, {"Control": ["Control-MACS2_callpeak_control62121_narrow_Peaks-peaks.bed"]}, {"Treated": ["Filter_SAM_or_BAM__N-bamcontrol.bam"]}, {"Treated": ["Filter_SAM_or_BAM__T-bamreads.bam"]}, {"Treated": ["Treated-MACS2_callpeak_on_T-peaks.bed"]}]]]' -o '/galaxy-repl/main/files/058/461/dataset_58461363.dat' -t 0.5 -f interval -p 'XXXX'  -n "8"

stderr

MACS2_callpeak_control62121_narrow_Peaks MACS2_callpeak_control62121_narrow_Peaks  Control  NA raw
MACS2_callpeak_on_T MACS2_callpeak_on_T  Treated  NA raw
Warning message:
No contrasts added. Perhaps try more categories, or lower value for minMembers. 
Error in pv.DBA(DBA, method, bSubControl, bFullLibrarySize, bTagwise = bTagwise,  : 
  Unable to perform analysis: no contrasts specified.
Calls: dba.analyze -> pv.DBA
Warning message:
No contrasts added. Perhaps try more categories, or lower value for minMembers.

stdout

[1] "en_US.UTF-8"

Job Information

None

Job Traceback

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1 Like
4

Hi @dush,
please have a look at this entry; it covers your case and provide some additional info about how to use Diffbind.

Regards

1 Like
5

Hi Cristóbal,

Thank you so much for the help. I also tried with 2 replicates before and gave the same error. But I didn’t use the name ‘Condition’. I will do that and update you.

Thanks again for the help.

Best regards
Dushani

2 Likes
6

Hi Cristóbal,

It worked.
Thank you!

Best regards
Dushani

2 Likes