Question: Need help with mpileup tool on Galaxy
0
gravatar for errityf
2.1 years ago by
errityf0
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 • 797 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by errityf0
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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. https://wiki.galaxyproject.org/Support#Reference_genomes

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

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 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 2.0 years ago by errityf0
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