Question: SAM Split tools only generate one split data
gravatar for kutan
15 months ago by
kutan0 wrote:

Hi there,

I'm using Galaxy to analyze my ChIP-seq data, but when I use NGS: SAMtools → Split to separate merged file into individual BAM files, only one dataset generated. Can you help me to fix it?


Best wishes, Kun

chip-seq • 461 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by kutan0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The tool splits based on differing read groups. Read groups would need to be added before the BAMs are merged. Most mapping tools include this option now do add at that step in the workflow, or you can use Picard's AddOrReplaceReadGroups to add this in any step prior to when the data is merged.

My guess is that your BAM dataset does not include read groups or that for some reason all are the same. Some modifications to your workflow are likely needed before using this tool.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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