Question: bam to fasta
gravatar for oliverh
2.1 years ago by
oliverh0 wrote:


I am very new to dealing with NGS data.  Have followed the instructions on how to get paired end data mapped to a reference genome (albeit one that is a related species).  Combined all the resulting bam files, cleaned it up but am stumped on how to get the resulting bam file into a fasta consensus.  I assume you use samtools and mpile but can't seem to get there.  Any suggestions.

Sorry if this is rather basic.



bowtie bam • 1.0k views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson24k • written 2.1 years ago by oliverh0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:


I am not sure if you are using RNA or DNA data, however to build up consensus transcripts or regions there are a few tools to pick from.

See the tool section "Assembly" in the Tool Shed. Some of these tools are on the public Main instance at, some are at other public servers, and the rest can be used in your own local or cloud Galaxy.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson24k
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