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Question: Making concensus sequence
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gravatar for guven.toksoy
3.7 years ago by
guven.toksoy • 0
Turkey
guven.toksoy • 0 wrote:

Hi, 

How can I make consensus sequence from Ion PGM reads as BAM format

G.Toksoy
bam • 586 views
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modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by guven.toksoy • 0
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are several tools in the "Assembly" section of the Tool Shed (for use in a local or cloud Galaxy). 
http://usegalaxy.org/toolshed
https://wiki.galaxyproject.org/ToolShed

Pick one that fits your data (Transcriptome, Whole Genome, etc). If the tool produces an alternate format (for example, if FASTQ is produced, convert to BAM format using existing wrapped tools such as those from Picard). Each 3rd party tool will have documentation about the data types appropriate for use. Reviewing publications that involve your specific datatype can also help guide you to the assembly tools to explore. If needed, one can also wrap pretty much any other tool for Galaxy, if programming resource is available. 

Thanks, Jen, Galaxy team

 
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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