Question: Question about Alignment of barcode sequence
gravatar for cupidboy818
4.1 years ago by
United States
cupidboy8180 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
ADD COMMENTlink modified 4.1 years ago by Jennifer Hillman Jackson25k • written 4.1 years ago by cupidboy8180
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
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