Question: Need help with mpileup tool on Galaxy
gravatar for errityf
2.5 years ago by
errityf0 wrote:

Hey, I'm new to bioinformatics and I'm having some trouble creating an mpileup. Trying to create an mpileup for a bam file. When I create one using the tool on samtools, using default settings it looks incorrect when I try to view it on IGV. I have viewed the .bam file on IGV before creating the mpileup and it looks ok. I would appreciate any help! Thanks.

galaxy mpileup samtools • 998 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by errityf0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The first thing to double check is that the proper reference genome was selected for the option "Using reference genome: ?". This should be the same exact genome build used to create the mapped BAM dataset.

If that does not resolve the problem, would you please explain more about what exactly is wrong and where you are working (Galaxy Main, a local, another public Galaxy instance). We may ask you to share a history from

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k

Hello Jen, Yes hg19 was used for BAM dataset and for subsequent analysis. I am doing a basic bioinformatics analysis research project for my masters degree. It requires me to align bam files and generate mpileup using samtools. The datasets are from an IonTorrent sequencer- I am wondering if this would cause any problems in the analysis? I uploaded bam files and converted them to FASTQ (as IonTorrent stores unaligned reads in bam format). I then aligned them generating bam file. Fiona

ADD REPLYlink written 2.5 years ago by errityf0
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