Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: mtDNA demo SAM to BAM problem GALAXY
0
gravatar for walshisjohn
3.1 years ago by
walshisjohn • 0
United States
walshisjohn • 0 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 • 720 views
ADD COMMENT • link •
modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by walshisjohn • 0
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for walshisjohn
3.1 years ago by
walshisjohn • 0
United States
walshisjohn • 0 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 COMMENT • link written 3.1 years ago by walshisjohn • 0
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: 175 users visited in the last hour