Question: Help with genomics courese question
gravatar for koylek
24 months ago by
koylek0 wrote:

Hello Biostar members, I am currently taking a course and we have some homework in which we need to upload data and create a workflow. It seems every time I try to run the data there is an error, so I am hoping someone can help? This is what I need to accomplish: I have all ready converted the data to be inputted I need to align my data to the dog(canFam3) reference sequence and convert the alignments to Bam Format. Next remove PCR Duplicates from the merged Bam File After this I need perform SNP discovery using either samtools, Mpileup or freebays on the BAM file created Then sort for quality and create a flatfile It appears that the final output file needs to be a .vcf file. Also, Turn in a summary file Hope this makes sense and I appreciate any help

galaxy • 588 views
ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by koylek0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The maintenance activities at Galaxy Main ( are causing failures, including upload failures. Full details are here:

I suggest waiting until the banner about maintenance on Main is removed before proceeding with the classwork.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k
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