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Question: barcode splitter- with barcode within sequence?
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gravatar for denizbombar
3.4 years ago by
denizbombar • 0
European Union
denizbombar • 0 wrote:

dear list,

i tried using the barcode splitter tool and it works fine for sequences where the barcode is right at the 5' beginning of the read. however, in many cases the reads start with a few random bases followed by the barcode- is there a way to let the barcode splitter (or another tool) reckognize these "hidden" barcodes as well?

I would greatly appreciate any hints

D
galaxy • 807 views
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modified 15 months ago by jixueli • 10 • written 3.4 years ago by denizbombar • 0
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

As far as I know, the tool has a fairly fixed set of usage parameters. But you could try trimming the sequences first (a few bases), testing, then allowing more mismatches, and testing again. Perhaps this will achieve what you need. For further advice, contacting the tool author - the link to his lab is at the bottom of the tool form - would be the best for specific advice for non-standard use cases.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for jixueli
15 months ago by
jixueli • 10
jixueli • 10 wrote:

Now I have the same issue described here. anyone has any suggestion?

ADD COMMENT • link written 15 months ago by jixueli • 10
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