Question: mtDNA demo SAM to BAM problem GALAXY
0
gravatar for walshisjohn
2.7 years ago by
United States
walshisjohn0 wrote:

Hello Folks,

I've been trying to run through the GALAXY.org mtDNA workflow demo, the first one, and cannot get past the SAM to BAM step. After filtering for unique reads, the SAM:BAM tool will not convert the SAM to BAM because the header is apparently gone. I tried the Reheader tool, but it errors because the source dataset is not a bam file.  

I'm following the demo steps exactly as presented and using the blood PCR1 demo dataset.  Is there a way around this?

Thanks John

galaxy samtools bam • 579 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by walshisjohn0
0
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This set of tutorials is based on Galaxy tools and code base that is a few years old. This means that a few adjustments will likely be needed.

In this case, first execute BWA for Illumina with one option changed. Choose to output the header.

Then after performing the select/filter step, add the header back to the SAM dataset using the tool Reheader copy SAM/BAM header between datasets. Then convert to BAM.

Let us know if you run into any other problems and we can help. Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
0
gravatar for walshisjohn
2.7 years ago by
United States
walshisjohn0 wrote:

Thanks Jennifer.  That's just what I tried a few times, without any luck.  The reheader job pauses and will not resume.  I also noticed that the reheader tool seems to require the target dataset to already be a bam.

I did notice that some of the tools had changed since the tutorial was created and figured they'd been around awhile...

John

 

 

 

 

ADD COMMENTlink written 2.7 years ago by walshisjohn0
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