How To Generate A Consensus Sequence On The Galaxy Platform

Question

[thelittledoctor]

Greetings,

I am attempting to generate a consensus sequence using the galaxy platform. I have been able to generate a pileup using Mpileup however I have been unable to generate a consensus sequence. I have tried using the instructions found in How to generate a consensus fasta sequence from SAM tools pileup? however Galaxy is not recognizing the results of the NGS: SAM Tools -> Pileup-to-Interval as a format that can be utilized for the final suggested step of Fetch Sequences -> Extract Genomic DNA. I have attempted to convert the data again to no avail. I'm at quite a loss at the moment. I would appreciate any insight or tips anyone could provide.

Thank you

[Matt Shirley]

I think you are confused about the "extract genomic DNA" tool. You supply a list of intervals and this tool will fetch the reference sequence between these coordinates. For generating a consensus sequence you'll need to take a different approach - one that I'm not sure you'll find in Galaxy.

Answer 1

[Joseph Hughes]

Generate the pileup from your bam file using "Generate pileup" and select the ten column pileup format. In this pileup, the fourth column corresponds to the consensus base. Using the cut columns 1 and 4 using "Text Manipulation>Cut" and then "Tabular-to-Fasta" you should get to what you want. Post your solution if you get it to work.

[Carlos Borroto]

"Generate pileup" uses "samtools pileup" command which is no longer available on recent versions of Samtools. I wonder if 'samtools mpileup" could be used in a similar way.

[Matt Shirley]

This looks like a good answer.