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Question: bam to fasta
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gravatar for oliverh
2.8 years ago by
oliverh • 0
oliverh • 0 wrote:

Hello,

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.

cheers,

oliver
bowtie bam • 1.6k views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by oliverh • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 http://usegalaxy.org, some are at other public servers, and the rest can be used in your own local or cloud Galaxy.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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