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Question: Question about Alignment of barcode sequence
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gravatar for cupidboy818
4.1 years ago by
cupidboy818 • 0
United States
cupidboy818 • 0 wrote:

For Ion torrent data (each read is like barcode sequence followed by target sequence)

I tried to use lastz and bowtie2 to just align the barcode sequence part onto barcode reference sequence, but there seems not to be any parameters for me to use to omit the following target sequence part. So this cause the alignment not to work.

Is there a way to do this alignment?

 

Thanks a lot!

 
barcodes tool alignment galaxy • 839 views
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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by cupidboy818 • 0
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gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For the tool's currently available on the public Main server, consider the following:

1. Use the barcode splitter to seperate the data into groups based on a common barcode (this is your goal?)

2. Then proceed with mapping the sequence data without barcodes, each group.

Other mappers (TMAP) are available in the Tool Shed for local or cloud Galaxy that may also be of help.
http://wiki.galaxyproject.org/BigPicture/Choices
http://usegalaxy.org/toolshed

Best, Jen, Galaxy team
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
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