Question: DiffBind differential binding analysis of ChIP-Seq peak data
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gravatar for franziska.froeb
5 months ago by
franziska.froeb0 wrote:

Hi,

I am analysing ChIPseq data on Galaxy beginning with raw fastq files (fastqc, trimmer by column, bowtie2, RmDup, Filter, bamcoverage, merge bam files + bamcoverage of merged files, MACS2 peak calling) and ending up with nice bigwig and bed files for visualizing in IGV. In the end, the goal would be to obtain a list of differentially bound regions because I am comparing wt with ko tissue. I found the nice sounding tool " DiffBind differential binding analysis of ChIP-Seq peak data " on Galaxy and I did this once with RStudio a couple of years ago, but unfortunately I have really problems picking the right bam files for that. Are those the one after "Filter"? The tool at Galaxy leaves me always with "tool error" and "This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help."

Could somebody please help me with that?

Thank you very much in advance!!!

Best wishes, Franziska

diffbind analysis chip-seq • 372 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by franziska.froeb0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Start troubleshooting by checking the input BAMs and other inputs for proper formatting as data issues can trigger this error: https://galaxyproject.org/support/tool-error/

There are a few Filter tools - and some can be configured or automatically remove the headers from BAM input/SAM output datasets. Those can have headers added back in with NGS: SAMtools > Reheader.

If you cannot figure out the usage problem and are working at Galaxy main https://usegalaxy.org, please send in the bug report and include a link to this biostars post.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
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