Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: SAM Split tools only generate one split data
0
gravatar for kutan
15 months ago by
kutan • 0
kutan • 0 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?

Thanks,

Best wishes, Kun

chip-seq • 461 views
ADD COMMENT • link •
modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by kutan • 0
0
gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour