Question: multi bam summary
gravatar for lnaren
6 months ago by
lnaren10 wrote:

Hello, I was trying to use mutibamsummary tool to generate the read coverage for 8 filtered Bam files(using SAMTOOLS, Filter SAM or BAM, output SAM or BAM ). These 8 filtered Bam files came from the ChIP seq data, which were mapped to the same genome(using Bowtie). But got error saying "No common chromosomes found". I was wondering why this happened? Also, is there any tutorials about detecting the methylation enrichment on histone by using ChIP seq analysis? Thank you very much, Ren

samtools sort error bam chip-seq • 275 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by lnaren10
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Did you sort the BAM datasets first? Was that successful?

If there is still a problem, and you can reproduce the problem at Galaxy Main, please send in a bug report. A tool problem is a possibility, and if present, we'll want to fix it. Please leave all inputs and outputs undeleted and include a link to this post in the comments.

I don't know of a Galaxy tutorial that covers that exact analysis. I linked in the current tutorials in the prior Q&A. If you are interested in helping to develop one, the Galaxy Training Network (GTN) would welcome contributions.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k

Hi Jen, The problem was solved after I used the BWA tool to do the mapping. I also sorted the bam file before using mutibamsummary tool.

Thank you very much, Ren

ADD REPLYlink written 6 months ago by lnaren10
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